Optical mapping and its potential for large-scale sequencing projects.

PubMed

Aston, C; Mishra, B; Schwartz, D C

1999-07-01

Physical mapping has been rediscovered as an important component of large-scale sequencing projects. Restriction maps provide landmark sequences at defined intervals, and high-resolution restriction maps can be assembled from ensembles of single molecules by optical means. Such optical maps can be constructed from both large-insert clones and genomic DNA, and are used as a scaffold for accurately aligning sequence contigs generated by shotgun sequencing.

High-Throughput Block Optical DNA Sequence Identification.

PubMed

Sagar, Dodderi Manjunatha; Korshoj, Lee Erik; Hanson, Katrina Bethany; Chowdhury, Partha Pratim; Otoupal, Peter Britton; Chatterjee, Anushree; Nagpal, Prashant

2018-01-01

Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm -1 . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probing orientation and rotation of red blood cells in optical tweezers by digital holographic microscopy

NASA Astrophysics Data System (ADS)

Cardenas, Nelson; Yu, Lingfeng; Mohanty, Samarendra K.

2011-03-01

Interaction of red blood cells (RBC) with optical tweezers has been found to differ under varied physiological and pathological conditions as compared to its normal conditions. Earlier, we reported difference in rotation of trapped RBC in hypertonic conditions for detection of malaria infection. Disk-like RBC when trapped in optical tweezers get oriented in the vertical plane to maximize interaction with trapping beam. However, classical bright field, phase contrast or epifluorescence microscopy cannot confirm its orientation, thus leading to ambiguous conclusions such as folding of RBC during trapping by some researchers. Now, with use of digital holographic microscopy (DHM), we achieved high axial sensitivity that confirmed orientation of trapped red blood cell. Further, DHM enabled quantitative phase imaging of RBC under hypertonic condition. Dynamic changes of rotating RBC under optical tweezers at different trapping laser power were evaluated by the use of DHM. The deviation from linear dependence of rotation speed of RBC on laser power, was attributed towards deformation of RBC shape due to higher laser power (or speed).

High-resolution imaging of the retinal nerve fiber layer in normal eyes using adaptive optics scanning laser ophthalmoscopy.

PubMed

Takayama, Kohei; Ooto, Sotaro; Hangai, Masanori; Arakawa, Naoko; Oshima, Susumu; Shibata, Naohisa; Hanebuchi, Masaaki; Inoue, Takashi; Yoshimura, Nagahisa

2012-01-01

To conduct high-resolution imaging of the retinal nerve fiber layer (RNFL) in normal eyes using adaptive optics scanning laser ophthalmoscopy (AO-SLO). AO-SLO images were obtained in 20 normal eyes at multiple locations in the posterior polar area and a circular path with a 3-4-mm diameter around the optic disc. For each eye, images focused on the RNFL were recorded and a montage of AO-SLO images was created. AO-SLO images for all eyes showed many hyperreflective bundles in the RNFL. Hyperreflective bundles above or below the fovea were seen in an arch from the temporal periphery on either side of a horizontal dividing line to the optic disc. The dark lines among the hyperreflective bundles were narrower around the optic disc compared with those in the temporal raphe. The hyperreflective bundles corresponded with the direction of the striations on SLO red-free images. The resolution and contrast of the bundles were much higher in AO-SLO images than in red-free fundus photography or SLO red-free images. The mean hyperreflective bundle width around the optic disc had a double-humped shape; the bundles at the temporal and nasal sides of the optic disc were narrower than those above and below the optic disc (P<0.001). RNFL thickness obtained by optical coherence tomography correlated with the hyperreflective bundle widths on AO-SLO (P<0.001) AO-SLO revealed hyperreflective bundles and dark lines in the RNFL, believed to be retinal nerve fiber bundles and Müller cell septa. The widths of the nerve fiber bundles appear to be proportional to the RNFL thickness at equivalent distances from the optic disc.

The effect of red light irradiation on spermatozoa DNA

NASA Astrophysics Data System (ADS)

Chow, Kay W.; Preece, Daryl; Gomez-Godinez, Veronica; Berns, Michael W.

2016-09-01

A key goal in the conservation of endangered species is to increase successful reproduction. In cases where traditional methods of in vitro fertilization are unsuccessful, new methods of assisted reproduction are needed. One option is selective fertilization via optically trapped sperm. A more passive option is red light irradiation. Red light irradiation has been shown to increase sperm motility, thus increasing fertilizing potential. However, there is some concern that exposure to laser irradiation induces the production of oxidative species in cells, which can be damaging to DNA. In order to test the safety of irradiating sperm, sperm samples were exposed to 633 nm laser light and their DNA were tested for oxidative damage. Using fluorescence microscopy, antibody staining, and ELISA to detect oxidative DNA damage, it was concluded that red light irradiation does not pose a safety risk to sperm DNA. The use of red light on sperm has potential in both animal conservation and human reproduction techniques. This method can also be used in conjunction with optical trapping for viable sperm selection.

[Molecular cloning of the DNA sequence of activin beta A subunit gene mature peptides from panda and related species and its application in the research of phylogeny and taxonomy].

PubMed

Wang, Xiao-Jing; Wang, Xiao-Xing; Wang, Ya-Jun; Wang, Xi-Zhong; He, Guang-Xin; Chen, Hong-Wei; Fei, Li-Song

2002-09-01

Activin, which is included in the transforming growth factor-beta (TGF beta) superfamily of proteins and receptors, is known to have broad-ranging effects in the creatures. The mature peptide of beta A subunit of this gene, one of the most highly conserved sequence, can elevate the basal secretion of follicle-stimulating hormone (FSH) in the pituitary and FSH is pivotal to organism's reproduction. Reproduction block is one of the main reasons which cause giant panda to extinct. The sequence of Activin beta A subunit gene mature peptides has been successfully amplified from giant panda, red panda and malayan sun bear's genomic DNA by using polymerase chain reaction (PCR) with a pair of degenerate primers. The PCR products were cloned into the vector pBlueScript+ of Esherichia coli. Sequence analysis of Activin beta A subunit gene mature peptides shows that the length of this gene segment is the same (359 bp) and there is no intron in all three species. The sequence encodes a peptide of 119 amino acid residues. The homology comparison demonstrates 93.9% DNA homology and 99% homology in amino acid among these three species. Both GenBank blast search result and restriction enzyme map reveal that the sequences of Activin beta A subunit gene mature peptides of different species are highly conserved during the evolution process. Phylogeny analysis is performed with PHYLIP software package. A consistent phylogeny tree has been drawn with three different methods. The software analysis outcome accords with the academic view that giant panda has a closer relationship to the malayan sun bear than the red panda. Giant panda should be grouped into the bear family (Uersidae) with the malayan sun bear. As to the red panda, it would be better that this animal be grouped into the unique family (red panda family) because of great difference between the red panda and the bears (Uersidae).

An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein

PubMed Central

Ando, Ryoko; Hama, Hiroshi; Yamamoto-Hino, Miki; Mizuno, Hideaki; Miyawaki, Atsushi

2002-01-01

We have cloned a gene encoding a fluorescent protein from a stony coral, Trachyphyllia geoffroyi, which emits green, yellow, and red light. The protein, named Kaede, includes a tripeptide, His-Tyr-Gly, that acts as a green chromophore that can be converted to red. The red fluorescence is comparable in intensity to the green and is stable under usual aerobic conditions. We found that the green-red conversion is highly sensitive to irradiation with UV or violet light (350–400 nm), which excites the protonated form of the chromophore. The excitation lights used to elicit red and green fluorescence do not induce photoconversion. Under a conventional epifluorescence microscope, Kaede protein expressed in HeLa cells turned red in a graded fashion in response to UV illumination; maximal illumination resulted in a 2,000-fold increase in the ratio of red-to-green signal. These color-changing properties provide a simple and powerful technique for regional optical marking. A focused UV pulse creates an instantaneous plane source of red Kaede within the cytosol. The red spot spreads rapidly throughout the cytosol, indicating its free diffusibility in the compartment. The extensive diffusion allows us to delineate a single neuron in a dense culture, where processes originating from many different somata are present. Illumination of a focused UV pulse onto the soma of a Kaede-expressing neuron resulted in filling of all processes with red fluorescence, allowing visualization of contact sites between the red and green neurons of interest. PMID:12271129

Genetic population structure of the lionfish Pterois miles (Scorpaenidae, Pteroinae) in the Gulf of Aqaba and northern Red Sea.

PubMed

Kochzius, Marc; Blohm, Dietmar

2005-03-14

The aim of this study is to reveal gene flow between populations of the coral reef dwelling lionfish Pterois miles in the Gulf of Aqaba and northern Red Sea. Due to the fjord-like hydrography and topology of the Gulf of Aqaba, isolation of populations might be possible. Analysis of 5' mitochondrial control region sequences from 94 P. miles specimens detected 32 polymorphic sites, yielding 38 haplotypes. Sequence divergence among different haplotypes ranged from 0.6% to 9.9% and genetic diversity was high (h=0.85, pi=1.9%). AMOVA indicates panmixia between the Gulf of Aqaba and northern Red Sea, but analysis of migration pattern shows an almost unidirectional migration originating from the Red Sea.

Genome Sequence of Acidovorax avenae Strain T10_61 Associated with Sugarcane Red Stripe in Argentina

PubMed Central

Fontana, Cecilia A.; Bassi, Daniela; Puglisi, Edoardo; Salazar, Sergio M.; Vignolo, Graciela M.; Coccocelli, Pier S.

2016-01-01

Red stripe of sugarcane in Argentina is a bacterial disease caused by Acidovorax avenae. The genome sequence from the first isolate of this bacterium in Argentina is presented here. The draft genome of the A. avenae T10_61 strain contains 5,646,552 bp and has a G+C content of 68.6 mol%. PMID:26847889

Rubrobacter-related bacteria associated with rosy discolouration of masonry and lime wall paintings.

PubMed

Schabereiter-Gurtner, C; Piñar, G; Vybiral, D; Lubitz, W; Rölleke, S

2001-11-01

A molecular approach was chosen to analyse the correlation between bacterial colonisation and rosy discolouration of masonry and lime wall paintings of two historically important buildings in Austria and Germany. The applied molecular method included PCR amplification of genes encoding the small subunit rRNA of bacteria (16S rDNA), genetic fingerprinting by denaturing gradient gel electrophoresis (DGGE), construction of 16S rDNA clone libraries, and comparative phylogenetic sequence analyses. The bacterial community of one red-pigmented biofilm sampled in Herberstein (Austria) contained bacteria phylogenetically related to the genera Saccharopolyspora, Nocardioides, Pseudonocardia, Rubrobacter, and to a Kineococcus-like bacterium. The bacterial community of the second red-pigmented biofilm sampled in Herberstein contained bacteria related to Arthrobacter, Comamonas, and to Rubrobacter. Rubrobacter-related 16S rDNA sequences were the most abundant. In the red-pigmented biofilm sampled in Burggen (Germany), only Rubrobacter-related bacteria were identified. No Rubrobacter-related bacteria were detected in non-rosy biofilms. The majority of sequences (70%) obtained from the bacterial communities of the three investigated rosy biofilms were related to sequences of the genus Rubrobacter (red-pigmented bacteria), demonstrating a correlation between Rubrobacter-related bacteria and the phenomenon of rosy discolouration of masonry and lime wall paintings.

Tests of two convection theories for red giant and red supergiant envelopes

NASA Technical Reports Server (NTRS)

Stothers, Richard B.; Chin, Chao-Wen

1995-01-01

Two theories of stellar envelope convection are considered here in the context of red giants and red supergiants of intermediate to high mass: Boehm-Vitense's standard mixing-length theory (MLT) and Canuto & Mazzitelli's new theory incorporating the full spectrum of turbulence (FST). Both theories assume incompressible convection. Two formulations of the convective mixing length are also evaluated: l proportional to the local pressure scale height (H(sub P)) and l proportional to the distance from the upper boundary of the convection zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red phase of core helium burning. Since the theoretically predicted effective temperatures for cool stars are known to be sensitive to the assigned value of the mixing length, this quantity has been individually calibrated for each evolutionary sequence. The calibration is done in a composite Hertzsprung-Russell diagram for the red giant and red supergiant members of well-observed Galactic open clusters. The MLT model requires the constant of proportionality for the convective mixing length to vary by a small but statistically significant amount with stellar mass, whereas the FST model succeeds in all cases with the mixing lenghth simply set equal to z. The structure of the deep stellar interior, however, remains very nearly unaffected by the choices of convection theory and mixing lenghth. Inside the convective envelope itself, a density inversion always occurs, but is somewhat smaller for the convectively more efficient MLT model. On physical grounds the FST model is preferable, and seems to alleviate the problem of finding the proper mixing length.

Adaptive Optics Near-Infrared Imaging of R136 in 30 Doradus: The Stellar Population of a Nearby Starburst

NASA Astrophysics Data System (ADS)

Brandl, B.; Sams, B. J.; Bertoldi, F.; Eckart, A.; Genzel, R.; Drapatz, S.; Hofmann, R.; Loewe, M.; Quirrenbach, A.

1996-07-01

We report 0".15 resolution near-infrared (NIR) imaging of R136, the central region of 30 Doradus in the large Magellanic Cloud. Our 12".8 x 12".8 images were recorded with the MPE camera SHARP II at the 3.6 m ESO telescope, using the adaptive optics system COME ON+. The high spatial resolution and sensitivity (20th magnitude in K) of our observations allow our H- and K-band images to be compared and combined with recent Hubble Space Telescope (HST) WFPC2 data of R136. We fit theoretical models with variable foreground extinction to the observed magnitudes of ˜1000 stars (roughly half of which were detected in HST and NIR bands) and derive the stellar population in this starburst region. We find no red giants or supergiants; however, we detect ˜110 extremely red sources which are probably young, pre-main-sequence low- or intermediate-mass stars. We obtained narrow-band images to identify known and new Wolf-Rayet stars by their He 11(2.189 μm) and Bry (2.166 μm) emission lines. The presence of W-R stars and absence of red supergiants narrow the cluster age to ˜3-5 Myr, while the derived ratio of W-R to 0 stars of 0.05 in the central region favors an age of 3.5 Myr, with a relatively short starburst duration. For the 0 stars, the core radius is found to be 0.1 pc and appears to decrease with increasing stellar mass. The slope of the mass function function is Γ = -1.6 on average, but it steepens with increasing distance from the cluster center from Γ = -1.3 in the inner 0.4 pc to Γ = -2.2 outside 0.8 pc for stars more massive than 12 Msun. The radial variation of the mass function reveals strong mass segregation that is probably due to the cluster's dynamical evolution.

Constraints on the Mass–Richness Relation from the Abundance and Weak Lensing of SDSS Clusters

NASA Astrophysics Data System (ADS)

Murata, Ryoma; Nishimichi, Takahiro; Takada, Masahiro; Miyatake, Hironao; Shirasaki, Masato; More, Surhud; Takahashi, Ryuichi; Osato, Ken

2018-02-01

We constrain the scaling relation between optical richness (λ) and halo mass (M) for a sample of Sloan Digital Sky Survey (SDSS) red-sequence Matched-filter Probabilistic Percolation (redMaPPer) galaxy clusters within the context of the Planck cosmological model. We use a forward modeling approach where we model the probability distribution of optical richness for a given mass, P({ln}λ | M). To model the abundance and the stacked lensing profiles, we use an emulator specifically built to interpolate the halo mass function and the stacked lensing profile for an arbitrary set of halo mass and redshift, which is calibrated based on a suite of high-resolution N-body simulations. We apply our method to 8312 SDSS redMaPPer clusters with 20 ≤ λ ≤ 100 and 0.10 ≤ z λ ≤ 0.33 and show that the lognormal distribution model for P(λ | M), with four free parameters, well reproduces the measured abundances and lensing profiles simultaneously. The constraints are characterized by the mean relation, < {ln}λ > (M)=A+B{ln}(M/{M}pivot}), with A={3.207}-0.046+0.044 and B={0.993}-0.055+0.041 (68% CL), where the pivot mass scale M pivot = 3 × 1014 h ‑1 M ⊙, and the scatter {σ }lnλ | M}={σ }0+q{ln}(M/{M}pivot}) with {σ }0={0.456}-0.039+0.047 and q=-{0.169}-0.026+0.035. We find that a large scatter in halo masses is required at the lowest-richness bins (20 ≤ λ ≲ 30) in order to reproduce the measurements. Without such a large scatter, the model prediction for the lensing profiles tends to overestimate the measured amplitudes. This might imply a possible contamination of intrinsically low-richness clusters due to the projection effects. Such a low-mass halo contribution is significantly reduced when applying our method to the sample of 30 ≤ λ ≤ 100.

In vivo vascular flow profiling combined with optical tweezers based blood routing

NASA Astrophysics Data System (ADS)

Meissner, Robert; Sugden, Wade W.; Siekmann, Arndt F.; Denz, Cornelia

2017-07-01

In vivo wall shear rate is quantified during zebrafish development using particle image velocimetry for biomedical diagnosis and modeling of artificial vessels. By using brightfield microscopy based high speed video tracking we can resolve single heart-beat cycles of blood flow in both space and time. Maximum blood flow velocities and wall shear rates are presented for zebrafish at two and three days post fertilization. By applying biocompatible optical tweezers as an Optical rail we present rerouting of red blood cells in vivo. With purely light-driven means we are able to compensate the lack of proper red blood cell blood flow in so far unperfused capillaries.

Optical Sensor based Chemical Modification as a Porous Cellulose Acetate Film and Its Application for Ethanol Sensor

NASA Astrophysics Data System (ADS)

Mulijani, S.; Iswantini, D.; Wicaksono, R.; Notriawan, D.

2018-03-01

A new approach to design and construction of an optical ethanol sensor has been developed by immobilizing a direct dye at a porous cellulosic polymer fllm. This sensor was fabricated by binding Nile Red to a cellulose acetate membrane that had previously been subjected to an exhaustive base hydrolysis. The prepared optical ethanol sensor was enhanced by adding pluronic as a porogen in the membrane. The addition of pluronic surfactant into cellulose acetate membrane increased the hydrophilic and porous properties of membrane. Advantageous features of the design include simple and easy of fabrication. Variable affecting sensor performance of dye concentration have been fully evaluated and optimized. The rapid response results from the porous structure of the polymeric support, which minimizes barriers to mass transport. Signal of optical sensor based on reaction of dye nile red over the membrane with ethanol and will produce the purple colored product. Result was obtained that maximum intensity of dye nile red reacted with alcohol is at 630-640 nm. Linear regression equation (r2), limit of detection, and limit of quantitation of membrane with 2% dye was 0.9625, 0.29%, and 0.97%. Performance of optical sensor was also evaluated through methanol, ethanol and propanol. This study was purposed to measure the polarity and selectivity of optic sensor toward the alcohol derivatives. Fluorescence intensity of optic sensor membrane for methanol 5%, ethanol 5% and propanol 5% was 15113.56, 16573.75 and 18495.97 respectively.

Contribution of Primordial Binary Evolution to the Two Blue-straggler Sequences in Globular Cluster M30

NASA Astrophysics Data System (ADS)

Jiang, Dengkai; Chen, Xuefei; Li, Lifang; Han, Zhanwen

2017-11-01

Two blue-straggler sequences discovered in globular cluster M30 provide a strong constraint on the formation mechanisms of blue stragglers. We study the formation of blue-straggler binaries through binary evolution, and find that binary evolution can contribute to the blue stragglers in both of the sequences. Whether a blue-straggler is located in the blue sequence or red sequence depends on the contribution of the mass donor to the total luminosity of the binary, which is generally observed as a single star in globular clusters. The blue stragglers in the blue sequence have a cool white dwarf companion, while the majority (˜60%) of the objects in the red sequence are binaries that are still experiencing mass transfer. However, there are also some objects for which the donors have just finished the mass transfer (the stripped-core stars, ˜10%) or the blue stragglers (the accretors) have evolved away from the blue sequence (˜30%). Meanwhile, W UMa contact binaries found in both sequences may be explained by various mass ratios, that is, W UMa contact binaries in the red sequence have two components with comparable masses (e.g., mass ratio q ˜ 0.3-1.0), while those in the blue sequence have low mass ratios (e.g., q< 0.3). However, the fraction of the blue sequence in M30 cannot be reproduced by binary population synthesis if we assumed the initial parameters of a binary sample to be the same as those of the field. This possibly indicates that dynamical effects on binary systems are very important in globular clusters.

The development of the red giant branch. I - Theoretical evolutionary sequences

NASA Technical Reports Server (NTRS)

Sweigart, Allen V.; Greggio, Laura; Renzini, Alvio

1989-01-01

A grid of 100 evolutionary sequences extending from the zero-age main sequence to the onset of helium burning has been computed for stellar masses between 1.4 and 3.4 solar masses, helium abundances of 0.20 and 0.30, and heavy-element abundances of 0.004, 0.01, and 0.04. Using these computations the transition in the morphology of the red giant branch (RGB) between low-mass stars, which have an extended and luminous first RGB phase prior to helium ignition, and intermediate-mass stars, which do not, is investigated. Extensive tabulations of the numerical results are provided to aid in applying these sequences. The effects of the first dredge-up on the surface helium and CNO abundances of the sequences is discussed.

Toxigenic Corynebacterium ulcerans isolated from a free-roaming red fox (Vulpes vulpes).

PubMed

Sting, Reinhard; Ketterer-Pintur, Sandra; Contzen, Matthias; Mauder, Norman; Süss-Dombrowski, Christine

2015-01-01

Corynebacterium (C.) ulcerans could be isolated from the spleen of a red fox (Vulpes vulpes) that had been found dead in the state of Baden-Württemberg, Germany. Pathohistological examination suggested that the fox had died of distemper, as was confirmed by PCR. The isolate was identified biochemically, by MALDI-TOF MS, FT-IR and by partial 16S rRNA, rpoB and tox gene sequencing. Using the Elek test the C. ulcerans isolate demonstrated diphtheria toxin production. FT-IR and sequencing data obtained from the C. ulcerans isolate from the red fox showed higher similarity to isolates from humans than to those from wild game.

Hepatozoon canis in German red foxes (Vulpes vulpes) and their ticks: molecular characterization and the phylogenetic relationship to other Hepatozoon spp.

PubMed

Najm, Nour-Addeen; Meyer-Kayser, Elisabeth; Hoffmann, Lothar; Pfister, Kurt; Silaghi, Cornelia

2014-07-01

In this study, the prevalence of Hepatozoon spp. in red foxes (Vulpes vulpes) and their ticks from Germany, as well as molecular characterizations and phylogenetic relationship to other Hepatozoon spp. were investigated. DNA extracts of 261 spleen samples and 1,953 ticks were examined for the presence of Hepatozoon spp. by a conventional polymerase chain reaction (PCR) targeting the 18S rRNA gene. The ticks included four tick species: Ixodes ricinus, Ixodes canisuga, Ixodes hexagonus and Dermacentor reticulatus. A total of 118/261 foxes (45.2%) and 148/1,953 ticks (7.5%) were Hepatozoon PCR-positive. Amplicons from 36 positive foxes and 41 positive ticks were sequenced. All sequences obtained from foxes and 39/41 from ticks had a 99% similarity to Hepatozoon canis, whereas two ticks' sequences had a 99% identity to Hepatozoon sp. The obtained Hepatozoon sequences in this study were phylogenetically related to other Hepatozoon sequences detected in other countries, which may represent strain variants. The high prevalence of H. canis DNA in red foxes in this study supports the suggested role of those animals in distribution of this parasite. Furthermore, detection of DNA of H. canis in foxes and all examined tick species collected from those foxes allows speculating about previously undescribed potential vectors for H. canis and suggests a potential role of the red fox in its natural endemic cycles.

Design and fabrication of optical chemical sensor for detection of nitroaromatic explosives based on fluorescence quenching of phenol red immobilized poly(vinyl alcohol) membrane.

PubMed

Zarei, Ali Reza; Ghazanchayi, Behnam

2016-04-01

The present study developed a new optical chemical sensor for detection of nitroaromatic explosives in liquid phase. The method is based on the fluorescence quenching of phenol red as fluorophore in a poly(vinyl alcohol) (PVA) membrane in the presence of nitroaromatic explosives as quenchers, e.g., 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (2,4-DNT), 4-nitrotoluene (4-NT), 2,4,6-trinitrobenzene (TNB), and nitrobenzene (NB). For chemical immobilization of phenol red in PVA, phenol red reacted with formaldehyde to produce hydroxymethyl groups and then attached to PVA membrane through the hydroxymethyl groups. The optical sensor showed strong quenching of nitroaromatic explosives. A Stern-Volmer graph for each explosive was constructed and showed that the range of concentration from 5.0 × 10(-6) to 2.5 × 10(-4) mol L(-1) was linear for each explosive and sensitivity varied as TNB >TNT>2,4-DNT>NB>4-NT. The response time of the sensor was within 1 min. The proposed sensor showed good reversibility and reproducibility. Copyright © 2015 Elsevier B.V. All rights reserved.

A High Affinity Red Fluorescence and Colorimetric Probe for Amyloid β Aggregates

NASA Astrophysics Data System (ADS)

Rajasekhar, K.; Narayanaswamy, Nagarjun; Murugan, N. Arul; Kuang, Guanglin; Ågren, Hans; Govindaraju, T.

2016-04-01

A major challenge in the Alzheimer’s disease (AD) is its timely diagnosis. Amyloid β (Aβ) aggregates have been proposed as the most viable biomarker for the diagnosis of AD. Here, we demonstrate hemicyanine-based benzothiazole-coumarin (TC) as a potential probe for the detection of highly toxic Aβ42 aggregates through switch-on, enhanced (~30 fold) red fluorescence (Emax = 654 nm) and characteristic colorimetric (light red to purple) optical outputs. Interestingly, TC exhibits selectivity towards Aβ42 fibrils compared to other abnormal protein aggregates. TC probe show nanomolar binding affinity (Ka = 1.72 × 107 M-1) towards Aβ42 aggregates and also displace ThT bound to Aβ42 fibrils due to its high binding affinity. The Aβ42 fibril-specific red-shift in the absorption spectra of TC responsible for the observed colorimetric optical output has been attributed to micro-environment change around the probe from hydrophilic-like to hydrophobic-like nature. The binding site, binding energy and changes in optical properties observed for TC upon interaction with Aβ42 fibrils have been further validated by molecular docking and time dependent density functional theory studies.

β-D-(1→4), β-D-(1→3) 'mixed linkage' xylans from red seaweeds of the order Nemaliales and Palmariales.

PubMed

Viana, Adriano G; Noseda, Miguel D; Gonçalves, Alan G; Duarte, Maria Eugênia R; Yokoya, Nair; Matulewicz, Maria C; Cerezo, Alberto S

2011-06-01

Xylans from five seaweeds belonging to the order Nemaliales (Galaxaura marginata, Galaxaura obtusata, Tricleocarpacylindrica, Tricleocarpa fragilis, and Scinaia halliae) and one of the order Palmariales (Palmaria palmata) collected on the Brazilian coasts were extracted with hot water and purified from acid xylomannans and/or xylogalactans through Cetavlon precipitation of the acid polysaccharides. The β-D-(1→4), β-D-(1→3) 'mixed linkage' structures were determined using methylation analysis and 1D and 2D NMR spectroscopy. The presence of large sequences of β-(1→4)-linked units suggests transient aggregates of ribbon- or helical-ordered structures that would explain the low optical rotations. Copyright © 2011 Elsevier Ltd. All rights reserved.

A gravitational lens candidate with an unusually red optical counterpart

NASA Technical Reports Server (NTRS)

Hewitt, J. N.; Turner, E. L.; Lawrence, C. R.; Schneider, D. P.; Brody, J. P.

1992-01-01

The properties of the strong radio source MG0414 + 0534 are described. It is found to display many of the properties expected in a gravitational lens system. At radio wavelengths and 0.5-arcsec resolution, MG0414 + 0534 is made up of four compact components whose unusual configuration and relative flux densities are similar to those found in confirmed four-image gravitational lens systems. At optical wavelengths three objects are detected, consistent with there being optical objects at the positions of the radio components, given the lower optical resolution. The radio and optical centroid positions agree within the astrometric errors, and the relative ordering of the fluxes is the same. The colors and radiooptical spectral indices are similar, but there are differences larger than the photometric errors and the measured variability (about 30 percent). Extinction by dust might simultaneously explain the unusually red color and the absence of light from a lens.

Radiation pressure on a biconcave human Red Blood Cell and the resulting deformation in a pair of parallel optical traps.

PubMed

Liao, Guan-Bo; Chen, Yin-Quan; Bareil, Paul B; Sheng, Yunlong; Chiou, Arthur; Chang, Ming-Shien

2014-10-01

We calculated the three-dimensional optical stress distribution and the resulting deformation on a biconcave human red blood cell (RBC) in a pair of parallel optical trap. We assumed a Gaussian intensity distribution with a spherical wavefront for each trapping beam and calculated the optical stress from the momentum transfer associated with the reflection and refraction of the incident photons at each interface. The RBC was modelled as a biconcave thin elastic membrane with uniform elasticity and a uniform thickness of 0.25 μm. The resulting cell deformation was determined from the optical stress distribution by finite element software, Comsol Structure Mechanics Module, with Young's modulus (E) as a fitting parameter in order to fit the theoretical results for cell elongation to our experimental data. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Photostable Silicon Rhodamine Platform for Optical Voltage Sensing

PubMed Central

Huang, Yi-Lin; Walker, Alison S.; Miller, Evan W.

2015-01-01

This paper describes the design and synthesis of a photostable, far-red to near-infrared (NIR) platform for optical voltage sensing. We developed a new, sulfonated silicon rhodamine fluorophore and integrated it with a phenylenevinylene molecular wire to create a Berkeley Red Sensor of Transmembrane potential, or BeRST 1 (“burst”). BeRST 1 is the first member of a class of farred to NIR voltage sensitive dyes that make use of a photoinduced electron transfer (PeT) trigger for optical interrogation of membrane voltage. We show that BeRST 1 displays bright, membrane-localized fluorescence in living cells, high photostability, and excellent voltage sensitivity in neurons. Depolarization of the plasma membrane results in rapid fluorescence increases (24% ΔF/F per 100 mV). BeRST 1 can be used in conjunction with fluorescent stains for organelles, Ca2+ indicators, and voltage-sensitive fluorescent proteins. In addition, the red-shifted spectral profile of BeRST 1, relative to commonly employed optogenetic actuators like ChannelRhodopsin2 (ChR2), which require blue light, enables optical electrophysiology in neurons. The high speed, sensitivity, photostability and long-wavelength fluorescence profiles of BeRST 1 make it a useful platform for the non-invasive, optical dissection of neuronal activity. PMID:26237573

21 CFR 1310.04 - Maintenance of records.

Code of Federal Regulations, 2010 CFR

2010-04-01

... salts, optical isomers and salts of optical isomers (ii) Red phosphorus (iii) White phosphorus (Other names: Yellow Phosphorus) (iv) Hypophosphorous acid and its salts (v) gamma-Butyrolactone (Other names...

Complete Mitochondrial Genome of the Red Fox (Vuples vuples) and Phylogenetic Analysis with Other Canid Species.

PubMed

Zhong, Hua-Ming; Zhang, Hong-Hai; Sha, Wei-Lai; Zhang, Cheng-De; Chen, Yu-Cai

2010-04-01

The whole mitochondrial genome sequence of red fox (Vuples vuples) was determined. It had a total length of 16 723 bp. As in most mammal mitochondrial genome, it contained 13 protein coding genes, two ribosome RNA genes, 22 transfer RNA genes and one control region. The base composition was 31.3% A, 26.1% C, 14.8% G and 27.8% T, respectively. The codon usage of red fox, arctic fox, gray wolf, domestic dog and coyote followed the same pattern except for an unusual ATT start codon, which initiates the NADH dehydrogenase subunit 3 gene in the red fox. A long tandem repeat rich in AC was found between conserved sequence block 1 and 2 in the control region. In order to confirm the phylogenetic relationships of red fox to other canids, phylogenetic trees were reconstructed by neighbor-joining and maximum parsimony methods using 12 concatenated heavy-strand protein-coding genes. The result indicated that arctic fox was the sister group of red fox and they both belong to the red fox-like clade in family Canidae, while gray wolf, domestic dog and coyote belong to wolf-like clade. The result was in accordance with existing phylogenetic results.

Missense polymorphisms in the MC1R gene of the dog, red fox, arctic fox and Chinese raccoon dog.

PubMed

Nowacka-Woszuk, J; Salamon, S; Gorna, A; Switonski, M

2013-04-01

Coat colour variation is determined by many genes, one of which is the melanocortin receptor type 1 (MC1R) gene. In this study, we examined the whole coding sequence of this gene in four species belonging to the Canidae family (dog, red fox, arctic fox and Chinese raccoon dog). Although the comparative analysis of the obtained nucleotide sequences revealed a high conservation, which varied between 97.9 and 99.1%, we altogether identified 22 SNPs (10 in dogs, six in farmed red foxes, two in wild red foxes, three in arctic foxes and one in Chinese raccoon dog). Among them, seven appeared to be novel: one silent in the dog, three missense and one silent in the red fox, one in the 3'-flanking region in the arctic fox and one silent in the Chinese raccoon dog. In dogs and red foxes, the SNPs segregated as 10 and four haplotypes, respectively. Taking into consideration the published reports and results of this study, the highest number of missense polymorphisms was until now found in the dog (9) and red fox (7). © 2012 Blackwell Verlag GmbH.

Normal and system lupus erythematosus red blood cell interactions studied by double trap optical tweezers: direct measurements of aggregation forces

NASA Astrophysics Data System (ADS)

Khokhlova, Maria D.; Lyubin, Eugeny V.; Zhdanov, Alexander G.; Rykova, Sophia Yu.; Sokolova, Irina A.; Fedyanin, Andrey A.

2012-02-01

Direct measurements of aggregation forces in piconewton range between two red blood cells in pair rouleau are performed under physiological conditions using double trap optical tweezers. Aggregation and disaggregation properties of healthy and pathologic (system lupus erythematosis) blood samples are analyzed. Strong difference in aggregation speed and behavior is revealed using the offered method which is proposed to be a promising tool for SLE monitoring at single cell level.

Seeing Red and Shooting Blanks: A Study of Red Quasars And Blank Field X-Ray Sources

NASA Technical Reports Server (NTRS)

Oliversen, Ronald J. (Technical Monitor); Elvis, Martin

2003-01-01

The primary source catalog of 'blanks' (bright ROSAT sources with no optical counterparts) has been published in the Astrophysical Journal. The first follow-up paper has also been published. This paper used a combination of ROSAT, Chandra and ground based data to convincingly identify one of the blanks as a Ultra-luminous X-ray source (ULX) in a spiral galaxy. A paper detailing optical and near-IR imaging observations of the remaining sources is underway.

Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.).

PubMed

Bushakra, Jill M; Lewers, Kim S; Staton, Margaret E; Zhebentyayeva, Tetyana; Saski, Christopher A

2015-10-26

Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders. Leaf and meristem tissue from 'Heritage' red raspberry (Rubus idaeus) and 'Bristol' black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs.  Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database. To accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species. This resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.

Isolation, sequencing and expression of RED, a novel human gene encoding an acidic-basic dipeptide repeat.

PubMed

Assier, E; Bouzinba-Segard, H; Stolzenberg, M C; Stephens, R; Bardos, J; Freemont, P; Charron, D; Trowsdale, J; Rich, T

1999-04-16

A novel human gene RED, and the murine homologue, MuRED, were cloned. These genes were named after the extensive stretch of alternating arginine (R) and glutamic acid (E) or aspartic acid (D) residues that they contain. We term this the 'RED' repeat. The genes of both species were expressed in a wide range of tissues and we have mapped the human gene to chromosome 5q22-24. MuRED and RED shared 98% sequence identity at the amino acid level. The open reading frame of both genes encodes a 557 amino acid protein. RED fused to a fluorescent tag was expressed in nuclei of transfected cells and localised to nuclear dots. Co-localisation studies showed that these nuclear dots did not contain either PML or Coilin, which are commonly found in the POD or coiled body nuclear compartments. Deletion of the amino terminal 265 amino acids resulted in a failure to sort efficiently to the nucleus, though nuclear dots were formed. Deletion of a further 50 amino acids from the amino terminus generates a protein that can sort to the nucleus but is unable to generate nuclear dots. Neither construct localised to the nucleolus. The characteristics of RED and its nuclear localisation implicate it as a regulatory protein, possibly involved in transcription.

The effects of a geometrical size, external electric fields and impurity on the optical gain of a quantum dot laser with a semi-parabolic spherical well potential

NASA Astrophysics Data System (ADS)

Owji, Erfan; Keshavarz, Alireza; Mokhtari, Hosein

2017-03-01

In this paper, a GaAs / Alx Ga1-x As quantum dot laser with a semi-parabolic spherical well potential is assumed. By using Runge-Kutta method the eigenenergies and the eigenstates of valence and conduct bands are obtained. The effects of geometrical sizes, external electric fields and hydrogen impurity on the different electronic transitions of the optical gain are studied. The results show that the optical gain peak increases and red-shifts, by increasing the width of well or barrier, while more increasing of the width causes blue-shift and decreases it. The hydrogen impurity decreases the optical gain peak and blue-shifts it. Also, the increasing of the external electric fields cause to increase the peak of the optical gain, and (blue) red shift it. Finally, the optical gain for 1s-1s and 2s-1s transitions is prominent, while it is so weak for other transitions.

Characterization of light absorption by chromophoric dissolved organic matter (CDOM) in the upper layer of the Red Sea

NASA Astrophysics Data System (ADS)

Kheireddine, Malika; Ouhssain, Mustapha; Calleja, Maria Ll.; Morán, Xosé Anxelu G.; Sarma, Y. V. B.; Tiwari, Surya P.; Jones, Burton H.

2018-03-01

The absorption coefficient of chromophoric dissolved organic matter (CDOM) is a major variable used in developing robust bio-optical models and understanding biogeochemical processes. Over the last decade, the optical properties of CDOM in the open sea have been intensely studied. However, their variations in clear water are poorly documented, particularly in the Red Sea, owing to the absence of in situ measurements. We performed several cruises in the Red Sea to investigate the spatial distribution of the absorption coefficient of CDOM. The spectral absorption coefficients were determined from 400 nm to 740 nm using a WETLabs ac-s hyper-spectral spectrophotometer. In general, we found a latitudinal gradient in the CDOM absorption coefficient at 443 nm (aCDOM(443)) from south to north that is likely influenced by the exchange of water through the strait of Bab-el-Mandeb and the thermohaline circulation of the Red Sea. However, high aCDOM(443) values were observed in the northern Red Sea due to the existence of a sub-mesoscale feature that may induce an increase in phytoplankton production and lead to CDOM production. The aCDOM(443) covaried with the chlorophyll a concentration ([Chl a],) despite a high scatter. Furthermore, the aCDOM(443) for a given [Chl a] concentration was higher than those predicted by global ocean bio-optical models. This study advances our understanding of CDOM concentration in the Red Sea and may help improve the accuracy of the algorithms used to obtain CDOM absorption from ocean color.

Complete mitochondrial genome of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis).

PubMed

Hu, Guang-Fu; Liu, Xiang-Jiang; Li, Zhong; Liang, Hong-Wei; Hu, Shao-Na; Zou, Gui-Wei

2016-01-01

The complete mitochondrial genomes of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis) were sequenced. Comparison of these two mitochondrial genomes revealed that the mtDNAs of these two common carp varieties were remarkably similar in genome length, gene order and content, and AT content. However, size variation between these two mitochondrial genomes presented here showed 39 site differences in overall length. About 2 site differences were located in rRNAs, 3 in tRNAs, 3 in the control region, 31 in protein-coding genes. Thirty-one variable bases in the protein-coding regions between the two varieties mitochondrial sequences led to three variable amino acids, which were mainly located in the protein ND5 and ND4.

Variations in thermo-optical properties of neutral red dye with laser ablated gold nanoparticles

NASA Astrophysics Data System (ADS)

Prakash, Anitha; Pathrose, Bini P.; Mathew, S.; Nampoori, V. P. N.; Radhakrishnan, P.; Mujeeb, A.

2018-05-01

We have investigated the thermal and optical properties of neutral red dye incorporated with different weight percentage of gold nanoparticles prepared by laser ablation method. Optical absorption studies confirmed the production of spherical nanoparticles and also the interactions of the dye molecules with gold nanoparticles. The quenching of fluorescence and the reduction in the lifetime of gold incorporated samples were observed and was due to the non-radiative energy transfer between the dye molecules and gold nanoparticles. Dual beam thermal lens technique has been employed to measure the heat diffusion in neutral red with various weight percentage of gold nano sol dispersed in ethanol. The significant outcome of the experiment is that, the overall heat diffusion is slower in the presence of gold nano sol compared to that of dye alone sample. Brownian motion is suggested to be the main mechanism of heat transfer under the present conditions. The thermal diffusivity variations of samples with respect to different excitation power of laser were also studied.

Polarized optical absorption and photoluminescence measurements in single-crystal thin films of 4'-dimethylamino-N-methyl-4-stilbazolium tosylate

NASA Astrophysics Data System (ADS)

Bhowmik, Achintya K.; Xu, Jianjun; Thakur, Mrinal

1999-11-01

Single-crystal thin films of the anhydrous (red) and the hydrated (orange) phases of the organic salt 4'-dimethylamino-N-methyl-4-stilbazolium tosylate were grown by a modification of the shear method. The optical absorption coefficients of the films were measured with light polarized along and normal to the dipole/molecular axis at both resonant and off-resonant wavelengths, and a strong dichroism was observed at the resonant wavelengths. The absorption measurements are important considering potential applications of these films (red phase) in high-speed single-pass thin-film electro-optic modulators [M. Thakur, J. Xu, A. Bhowmik, and L. Zhou, Appl. Phys. Lett. 74, 635 (1999)] and other photonic devices. Highly polarized photoluminescence (PL) has been observed in these films. The PL efficiencies of the red- and orange-phase single-crystal films were measured to be about 12% and 14%, respectively, which are significantly higher than the maximum PL efficiency measured in solution (3%).

Genome organization and DNA methylation patterns of B chromosomes in the red fox and Chinese raccoon dogs.

PubMed

Bugno-Poniewierska, Monika; Solek, Przemysław; Wronski, Mariusz; Potocki, Leszek; Jezewska-Witkowska, Grażyna; Wnuk, Maciej

2014-12-01

The molecular structure of B chromosomes (Bs) is relatively well studied. Previous research demonstrates that Bs of various species usually contain two types of repetitive DNA sequences, satellite DNA and ribosomal DNA, but Bs also contain genes encoding histone proteins and many others. However, many questions remain regarding the origin and function of these chromosomes. Here, we focused on the comparative cytogenetic characteristics of the red fox and Chinese raccoon dog B chromosomes with particular attention to the distribution of repetitive DNA sequences and their methylation status. We confirmed that the small Bs of the red fox show a typical fluorescent telomeric distal signal, whereas medium-sized Bs of the Chinese raccoon dog were characterized by clusters of telomeric sequences along their length. We also found different DNA methylation patterns for the B chromosomes of both species. Therefore, we concluded that DNA methylation may maintain the transcriptional inactivation of DNA sequences localized to B chromosomes and may prevent genetic unbalancing and several negative phenotypic effects. © 2014 The Authors.

Morphological analysis of red blood cells by polychromatic interference microscopy of thin films

NASA Astrophysics Data System (ADS)

Dyachenko, A. A.; Malinova, L. I.; Ryabukho, V. P.

2016-11-01

Red blood cells (RBC) distribution width (RDW) is a promising hematological parameter with broadapplications in clinical practice; in various studies RDWhas been shown to be associated with increased risk of heart failure (HF) in general population. It predicts mortality and other major adverse events in HF patients. In this report new method of RDWmeasurement is presented. It's based on interference color analysis of red blood cells in blood smear and further measurement of its optical thickness. Descriptive statistics of the of the RBC optical thickness distribution in a blood smear were used for RDW estimation in every studied sample. Proposed method is considered to be avoiding type II errors and minimizing the variability of measured RDW.

Development and transferability of black and red raspberry microsatellite markers from short-read sequences

USDA-ARS?s Scientific Manuscript database

The advent of next-generation sequencing technologies has been a boon to the cost-effective development of molecular markers, particularly in non-model species. Here, we demonstrate the efficiency of microsatellite or simple sequence repeat (SSR) marker development from short-read sequences using th...

Optical efficiency enhancement in white organic light-emitting diode display with high color gamut using patterned quantum dot film and long pass filter

NASA Astrophysics Data System (ADS)

Kim, Hyo-Jun; Shin, Min-Ho; Kim, Young-Joo

2016-08-01

A new structure for white organic light-emitting diode (OLED) displays with a patterned quantum dot (QD) film and a long pass filter (LPF) was proposed and evaluated to realize both a high color gamut and high optical efficiency. Since optical efficiency is a critical parameter in white OLED displays with a high color gamut, a red or green QD film as a color-converting component and an LPF as a light-recycling component are introduced to be adjusted via the characteristics of a color filter (CF). Compared with a conventional white OLED without both a QD film and the LPF, it was confirmed experimentally that the optical powers of red and green light in a new white OLED display were increased by 54.1 and 24.7% using a 30 wt % red QD film and a 20 wt % green QD film with the LPF, respectively. In addition, the white OLED with both a QD film and the LPF resulted in an increase in the color gamut from 98 to 107% (NTSC x,y ratio) due to the narrow emission linewidth of the QDs.

Utilization of a new optical sensor unit to monitor the electrochemical elimination of selected dyes in water

NASA Astrophysics Data System (ADS)

Valica, M.; Černá, T.; Hostin, S.

2017-10-01

This paper presents results obtained by developed optical sensor, which consist from multi-wavelength LED light source and two photodetectors capable of measuring the change in optical signal along two different optical paths (absorbance and reflectance measurements). Arduino microcomputer was used for light source management and optical signal data measuring and recording. Analytical validation of developed optical sensor is presented in this paper. The performance of the system has been tested with varying water solution of dyes (malachite green, methyl orange, trypan red). These results show strong correlations between the optical signal response and colour change from the dyes. Sensor was used for continual in-situ monitoring of electrochemical elimination of selected dyes (current density 15.7 mA cm-2, electrolyte volume 4 L and NaCl concentration 2 g L-1). Maximum decolorization level varies with each dye. For malachite green was obtain 92,7 % decolorization (25 min); methyl orange 90,8% (8,5 min) and trypan red 84,7% decolorization after 33 min of electrochemical treatment.

Galaxy Zoo: evidence for diverse star formation histories through the green valley

NASA Astrophysics Data System (ADS)

Smethurst, R. J.; Lintott, C. J.; Simmons, B. D.; Schawinski, K.; Marshall, P. J.; Bamford, S.; Fortson, L.; Kaviraj, S.; Masters, K. L.; Melvin, T.; Nichol, R. C.; Skibba, R. A.; Willett, K. W.

2015-06-01

Does galaxy evolution proceed through the green valley via multiple pathways or as a single population? Motivated by recent results highlighting radically different evolutionary pathways between early- and late-type galaxies, we present results from a simple Bayesian approach to this problem wherein we model the star formation history (SFH) of a galaxy with two parameters, [t, τ] and compare the predicted and observed optical and near-ultraviolet colours. We use a novel method to investigate the morphological differences between the most probable SFHs for both disc-like and smooth-like populations of galaxies, by using a sample of 126 316 galaxies (0.01 < z < 0.25) with probabilistic estimates of morphology from Galaxy Zoo. We find a clear difference between the quenching time-scales preferred by smooth- and disc-like galaxies, with three possible routes through the green valley dominated by smooth- (rapid time-scales, attributed to major mergers), intermediate- (intermediate time-scales, attributed to minor mergers and galaxy interactions) and disc-like (slow time-scales, attributed to secular evolution) galaxies. We hypothesize that morphological changes occur in systems which have undergone quenching with an exponential time-scale τ < 1.5 Gyr, in order for the evolution of galaxies in the green valley to match the ratio of smooth to disc galaxies observed in the red sequence. These rapid time-scales are instrumental in the formation of the red sequence at earlier times; however, we find that galaxies currently passing through the green valley typically do so at intermediate time-scales.†

Science from a glimpse: Hubble SNAPshot observations of massive galaxy clusters

NASA Astrophysics Data System (ADS)

Repp, A.; Ebeling, H.

2018-06-01

Hubble Space Telescope SNAPshot surveys of 86 X-ray selected galaxy clusters at 0.3 < z < 0.5 from the MACS sample have proven invaluable for the exploration of a wide range of astronomical research topics. We here present an overview of the four MACS SNAPshot surveys conducted from Cycle 14 to Cycle 20 as part of a long-term effort aimed at identifying exceptional cluster targets for in-depth follow up by the extragalactic community. We also release redshifts and X-ray luminosities of all clusters observed as part of this initiative. To illustrate the power of SNAPshot observations of MACS clusters, we explore several aspects of galaxy evolution illuminated by the images obtained for these programmes. We confirm the high lensing efficiency of X-ray selected clusters at z > 0.3. Examining the evolution of the slope of the cluster red sequence, we observe at best a slight decrease with redshift, indicating minimal age contribution since z ˜ 1. Congruent to previous studies' findings, we note that the two BCGs which are significantly bluer (≥5σ) than their clusters' red sequences reside in relaxed clusters and exhibit pronounced internal structure. Thanks to our targets' high X-ray luminosity, the subset of our sample observed with Chandra adds valuable leverage to the X-ray luminosity-optical richness relation, which, albeit with substantial scatter, is now clearly established from groups to extremely massive clusters of galaxies. We conclude that SNAPshot observations of MACS clusters stand to continue to play a vital pathfinder role for astrophysical investigations across the entire electromagnetic spectrum.

Multianalyte, dipstick-type, nanoparticle-based DNA biosensor for visual genotyping of single-nucleotide polymorphisms.

PubMed

Litos, Ioannis K; Ioannou, Penelope C; Christopoulos, Theodore K; Traeger-Synodinos, Jan; Kanavakis, Emmanuel

2009-06-15

DNA biosensors involve molecular recognition of the target sequence by hybridization with specific probes and detection by electrochemical, optical or gravimetric transduction. Disposable, dipstick-type biosensors have been developed recently, which enable visual detection of DNA without using instruments. In this context, we report a multianalyte DNA biosensor for visual genotyping of two single-nucleotide polymorphisms (SNPs). As a model, the biosensor was applied to the simultaneous genotyping of two SNPs, entailing the detection of four alleles. A PCR product that flanks both polymorphic sites is subjected to a single primer extension (PEXT) reaction employing four allele-specific primers, each containing a region complementary to an allele and a characteristic segment that enables subsequent capture on a test zone of the biosensor. The primers are extended with dNTPs and biotin-dUTP only if there is perfect complementarity with the interrogated sequence. The PEXT mixture is applied to the biosensor. As the developing buffer migrates along the strip, all the allele-specific primers are captured by immobilized oligonucleotides at the four test zones of the biosensor and detected by antibiotin-functionalized gold nanoparticles. As a result, the test zones are colored red if extension has occurred denoting the presence of the corresponding allele in the original sample. The excess nanoparticles are captured by immobilized biotinylated albumin at the control zone of the sensor forming another red zone that indicates the proper performance of the system. The assay was applied successfully to the genotyping of twenty clinical samples for two common SNPs of MBL2 gene.

Pyrosequencing of the northern red oak (Quercus rubra L.) chloroplast genome reveals high quality polymorphisms for population management

Treesearch

Lisa W. Alexander; Keith E. Woeste

2014-01-01

Given the low intraspecific chloroplast diversity detected in northern red oak (Quercus rubra L.), more powerful genetic tools are necessary to accurately characterize Q. rubra chloroplast diversity and structure. We report the sequencing, assembly, and annotation of the chloroplast genome of northern red oak via pyrosequencing and...

Amplification of North American Red Oak Microsatellite Markers in European White Oaks and Chinese Chestnut

Treesearch

P. R. Aldrich; M. Jagtap; C. H. Michler; J. Romero-Severson

2003-01-01

We examined the cross-species amplification success of thirty microsatellite markers developed from North American northern red oak (Quercus rubra) in other members of the family Fagaceae. Sixteen of these markers are newly developed and we report primer sequences and amplification conditions here. Twelve of the thirty (40.0%) red oak markers...

Bright and photostable cyanine-styryl chromophores with green and red fluorescence colour for DNA staining

NASA Astrophysics Data System (ADS)

Bohländer, Peggy R.; Wagenknecht, Hans-Achim

2015-12-01

The synthesis and optical characterisation of a series of green- and red-emitting cyanine and cyanine-styryl dyes is presented that were developed based on the cyanine-indole-quinolinium and based on the thiazole red type structure. For the green emitting fluorophores the quinolinium part was replaced by a pyridinium group. The bridge to the indole group was attached either to the 2-position or to the 4-position of the pyridinium moiety. For the red-emitting dyes the connection to the indole moiety is at the 4-position of the quinolinium part. In each set of dyes a methyl group at the indole-NH and/or a phenyl group at the 2-position of the indole part were introduced to tune the optical properties and photostability. Additionally, two dyes were modified with a cyano group to tune the photophysical properties and to enhance the photostabilities. The developed dyes show good photostabilities and bright green or red fluorescence intensities in the presence of DNA. Thus, these dyes represent important and promising candidates for fluorescent molecular imaging of nucleic acids inside living cells.

Galactic Gathering Gives Impressive Light Display

NASA Image and Video Library

2014-12-11

This composite image of NGC 2207 and IC 2163 contains Chandra data in pink, optical-light data from NASA Hubble Space Telescope in red, green, and blue appearing as blue, white, orange, and brown, and infrared data from Spitzer Space Telescope in red.

Mutant swarms of a totivirus-like entities are present in the red macroalga Chondrus crispus and have been partially transferred to the nuclear genome.

PubMed

Rousvoal, Sylvie; Bouyer, Betty; López-Cristoffanini, Camilo; Boyen, Catherine; Collén, Jonas

2016-08-01

Chondrus crispus Stackhouse (Gigartinales) is a red seaweed found on North Atlantic rocky shores. Electrophoresis of RNA extracts showed a prominent band with a size of around 6,000 bp. Sequencing of the band revealed several sequences with similarity to totiviruses, double-stranded RNA viruses that normally infect fungi. This virus-like entity was named C. crispus virus (CcV). It should probably be regarded as an extreme viral quasispecies or a mutant swarm since low identity (<65%) was found between sequences. Totiviruses typically code for two genes: one capsid gene (gag) and one RNA-dependent RNA polymerase gene (pol) with a pseudoknot structure between the genes. Both the genes and the intergenic structures were found in the CcV sequences. A nonidentical gag gene was also found in the nuclear genome of C. crispus, with associated expressed sequence tags (EST) and upstream regulatory features. The gene was presumably horizontally transferred from the virus to the alga. Similar dsRNA bands were seen in extracts from different life cycle stages of C. crispus and from all geographic locations tested. In addition, similar bands were also observed in RNA extractions from other red algae; however, the significance of this apparently widespread phenomenon is unknown. Neither phenotype caused by the infection nor any virus particles or capsid proteins were identified; thus, the presence of viral particles has not been validated. These findings increase the known host range of totiviruses to include marine red algae. © 2016 Phycological Society of America.

BIO-OPTICAL CHARACTERIZATION OF THE DINOFLAGELLATE GYMNODINIUM BREVE AND THE DIATOM THALASSIOSIRA WEISSFLOGII IN OUTDOOR TANKS

EPA Science Inventory

The bio-optical signatures of harmful algal blooms can be used to define ocean color satellite algorithms. We characterized the bio-optical properties of nutrient-replete cultures of the red tide dinoflagellate Gymnodinium breve and the diatom Thalassiosira weissflogii. We cultur...

Optical Searches for Baryonic Dark Matter

NASA Astrophysics Data System (ADS)

Graff, David Steven

1997-08-01

Microlensing results suggest that a good fraction of the halo is composed of massive chunks (0.1-1 Msolar) called MACHOs. I examine several optical searches for dim stars to constrain the local density of MACHOs. These searches show that (1) there are few red dwarfs in the galactic halo, and (2) they suggest that there are few brown dwarfs. I also find that (3) there may be sufficiently many white dwarfs in the halo to account for the microlensing results, but only if certain interesting conditions are met. (1) I examine a deep search for halo red dwarfs (Bahcall, Flynn, Gould & Kirhakos 1994). Using new stellar models and parallax observations of low mass, low metallicity stars, I find the halo red dwarf density to be <1% of the halo, while my best estimate of this value is 0.14-0.37%. (2) I derive mass functions (MF) for halo red dwarfs (the faintest hydrogen burning stars) and then extrapolate to place limits on the total mass of halo brown dwarfs (stars not quite massive enough to burn hydrogen). I find that the MF for halo red dwarfs cannot rise more quickly than 1/m2 as one approaches the hydrogen burning limit. Using recent results from star formation theory, I extrapolate the MF into the brown-dwarf regime. Likely extrapolations imply that the total mass of brown dwarfs in the halo is less than ~3% of the local mass density of the halo (~0.3% for the more realistic models I consider). My limits apply to brown dwarfs in the halo that come from the same stellar population as the red dwarfs. (3) A ground based search by Liebert, Dahn & Monet (1988) and a search of the Hubble Deep Field by Flynn, Bahcall & Gould (1996) have found no evidence for a substantial halo population of white dwarfs, implying that the putative halo population is either dim enough or sparse enough to elude detection. I use white dwarf luminosity functions calculated from various main sequence progenitor mass functions to re-examine the implications of these searches in light of recent microlensing results. I show that the minimum age of the white dwarf population depends upon assumptions regarding the initial mass function, atmospheric composition, and their total density. When I compare various theoretical white dwarf luminosity functions in which I vary these three parameters with the non detections of Liebert et al. and Flynn et al., I conclude that if white dwarfs constitute a significant portion of the halo then (I) the Universe must be 11 Gyr old and (II) they must have helium dominated atmospheres. Thus, white dwarfs could be the MACHOs and could make a significant contribution to galactic dark matter.

Deep sequencing and proteomic analysis of the microRNA-induced silencing complex in human red blood cells.

PubMed

Azzouzi, Imane; Moest, Hansjoerg; Wollscheid, Bernd; Schmugge, Markus; Eekels, Julia J M; Speer, Oliver

2015-05-01

During maturation, erythropoietic cells extrude their nuclei but retain their ability to respond to oxidant stress by tightly regulating protein translation. Several studies have reported microRNA-mediated regulation of translation during terminal stages of erythropoiesis, even after enucleation. In the present study, we performed a detailed examination of the endogenous microRNA machinery in human red blood cells using a combination of deep sequencing analysis of microRNAs and proteomic analysis of the microRNA-induced silencing complex. Among the 197 different microRNAs detected, miR-451a was the most abundant, representing more than 60% of all read sequences. In addition, miR-451a and its known target, 14-3-3ζ mRNA, were bound to the microRNA-induced silencing complex, implying their direct interaction in red blood cells. The proteomic characterization of endogenous Argonaute 2-associated microRNA-induced silencing complex revealed 26 cofactor candidates. Among these cofactors, we identified several RNA-binding proteins, as well as motor proteins and vesicular trafficking proteins. Our results demonstrate that red blood cells contain complex microRNA machinery, which might enable immature red blood cells to control protein translation independent of de novo nuclei information. Copyright © 2015 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.

Sequence analysis of a canine parvovirus isolated from a red panda (Ailurus fulgens) in China.

PubMed

Qin, Qin; Loeffler, I Kati; Li, Ming; Tian, Kegong; Wei, Fuwen

2007-06-01

Canine parvovirus (CPV) was first recognized in the late 1970 s in dogs and has mutated and spread throughout the world in canid and felid species since then. In this study, a novel CPV was isolated from the endangered red panda (Ailurus fulgens) in China. Nucleotide and phylogenetic analysis of the capsid protein VP2 gene classified the red panda parvovirus (RPPV) as a CPV-2a type. Substitution of Val for Gly at the conserved 300 residue in RPPV presents an unusual variation in the CPV-2a amino acid sequence and is further evidence for the continuing evolution of the virus. The 300 residue is important in distinguishing the antigenicity and host range of CPVs. The clinical significance and population impact of RPPV infection in captive red pandas in China is unknown and is an important topic for future research.

Draft genome of the red harvester ant Pogonomyrmex barbatus.

PubMed

Smith, Chris R; Smith, Christopher D; Robertson, Hugh M; Helmkampf, Martin; Zimin, Aleksey; Yandell, Mark; Holt, Carson; Hu, Hao; Abouheif, Ehab; Benton, Richard; Cash, Elizabeth; Croset, Vincent; Currie, Cameron R; Elhaik, Eran; Elsik, Christine G; Favé, Marie-Julie; Fernandes, Vilaiwan; Gibson, Joshua D; Graur, Dan; Gronenberg, Wulfila; Grubbs, Kirk J; Hagen, Darren E; Viniegra, Ana Sofia Ibarraran; Johnson, Brian R; Johnson, Reed M; Khila, Abderrahman; Kim, Jay W; Mathis, Kaitlyn A; Munoz-Torres, Monica C; Murphy, Marguerite C; Mustard, Julie A; Nakamura, Rin; Niehuis, Oliver; Nigam, Surabhi; Overson, Rick P; Placek, Jennifer E; Rajakumar, Rajendhran; Reese, Justin T; Suen, Garret; Tao, Shu; Torres, Candice W; Tsutsui, Neil D; Viljakainen, Lumi; Wolschin, Florian; Gadau, Jürgen

2011-04-05

We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.

PubMed

Rando, Halie M; Farré, Marta; Robson, Michael P; Won, Naomi B; Johnson, Jennifer L; Buch, Ronak; Bastounes, Estelle R; Xiang, Xueyan; Feng, Shaohong; Liu, Shiping; Xiong, Zijun; Kim, Jaebum; Zhang, Guojie; Trut, Lyudmila N; Larkin, Denis M; Kukekova, Anna V

2018-06-20

The genome of a red fox ( Vulpes vulpes ) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.

Photographic Film Image Enhancement

DOT National Transportation Integrated Search

1975-01-01

A series of experiments were undertaken to assess the feasibility of defogging color film by the techniques of Optical Spatial Filtering. A coherent optical processor was built using red, blue, and green laser light input and specially designed Fouri...

Serological and molecular epidemiology of canine adenovirus type 1 in red foxes (Vulpes vulpes) in the United Kingdom.

PubMed

Walker, David; Fee, Seán A; Hartley, Gill; Learmount, Jane; O'Hagan, Maria J H; Meredith, Anna L; de C Bronsvoort, Barend M; Porphyre, Thibaud; Sharp, Colin P; Philbey, Adrian W

2016-10-31

Canine adenovirus type 1 (CAV-1) causes infectious canine hepatitis (ICH), a frequently fatal disease which primarily affects canids. In this study, serology (ELISA) and molecular techniques (PCR/qPCR) were utilised to investigate the exposure of free-ranging red foxes (Vulpes vulpes) to CAV-1 in the United Kingdom (UK) and to examine their role as a wildlife reservoir of infection for susceptible species. The role of canine adenovirus type 2 (CAV-2), primarily a respiratory pathogen, was also explored. In foxes with no evidence of ICH on post-mortem examination, 29 of 154 (18.8%) red foxes had inapparent infections with CAV-1, as detected by a nested PCR, in a range of samples, including liver, kidney, spleen, brain, and lung. CAV-1 was detected in the urine of three red foxes with inapparent infections. It was estimated that 302 of 469 (64.4%) red foxes were seropositive for canine adenovirus (CAV) by ELISA. CAV-2 was not detected by PCR in any red foxes examined. Additional sequence data were obtained from CAV-1 positive samples, revealing regional variations in CAV-1 sequences. It is concluded that CAV-1 is endemic in free-ranging red foxes in the UK and that many foxes have inapparent infections in a range of tissues.

Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609.

PubMed

Sambles, Christine; Middelhaufe, Sabine; Soanes, Darren; Kolak, Dagmara; Lux, Thomas; Moore, Karen; Matoušková, Petra; Parker, David; Lee, Rob; Love, John; Aves, Stephen J

2017-09-01

Most eukaryotic oleaginous species are yeasts and among them the basidiomycete red yeast, Rhodotorula ( Rhodosporidium ) toruloides (Pucciniomycotina) is known to produce high quantities of lipids when grown in nitrogen-limiting media, and has potential for biodiesel production. The genome of the CGMCC 2.1609 strain of this oleaginous red yeast was sequenced using a hybrid of Roche 454 and Illumina technology generating 13 × coverage. The de novo assembly was carried out using MIRA and scaffolded using MAQ and BAMBUS. The sequencing and assembly resulted in 365 scaffolds with total genome size of 33.4 Mb. The complete genome sequence of this strain was deposited in GenBank and the accession number is LKER00000000. The annotation is available on Figshare (doi:10.6084/m9.figshare.4754251).

Genome survey sequencing of red swamp crayfish Procambarus clarkii.

PubMed

Shi, Linlin; Yi, Shaokui; Li, Yanhe

2018-06-21

Red swamp crayfish, Procambarus clarkii, presently is an important aquatic commercial species in China. The crayfish is a hot area of research focus, and its genetic improvement is quite urgent for the crayfish aquaculture in China. However, the knowledge of its genomic landscape is limited. In this study, a survey of P. clarkii genome was investigated based on Illumina's Solexa sequencing platform. Meanwhile, its genome size was estimated using flow cytometry. Interestingly, the genome size estimated is about 8.50 Gb by flow cytometry and 1.86 Gb with genome survey sequencing. Based on the assembled genome sequences, total of 136,962 genes and 152,268 exons were predicted, and the predicted genes ranged from 150 to 12,807 bp in length. The survey sequences could help accelerate the progress of gene discovery involved in genetic diversity and evolutionary analysis, even though it could not successfully applied for estimation of P. clarkii genome size.

Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug)

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

Stackebrandt, Erko; Zeytun, Ahmet; Lapidus, Alla L.

2013-01-01

Coriobacterium glomerans Haas and Ko nig 1988, is the only species of the genus Coriobacterium, family Coriobacteriaceae, order Coriobacteriales, phylum Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs, i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the genome of strain PW2T is its endosymbiotic life style which is rare among members of Actinobacteria. Here we describe the features of this symbiont, together with the complete genome sequence and its annotation. This is the first complete genome sequence of a member of the genus Coriobacterium and the sixth member of the order Coriobacteriales for whichmore » complete genome sequences are now available. The 2,115,681 bp long single replicon genome with its 1,804 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

First report of Enterocytozoon bieneusi from giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens) in China.

PubMed

Tian, Ge-Ru; Zhao, Guang-Hui; Du, Shuai-Zhi; Hu, Xiong-Feng; Wang, Hui-Bao; Zhang, Long-Xian; Yu, San-Ke

2015-08-01

Enterocytozoon bieneusi is an emerging and opportunistic enteric pathogen triggering diarrhea and enteric disease in humans and animals. Despite extensive research on this pathogen, the prevalence and genotypes of E. bieneusi infection in precious wild animals of giant and red pandas have not been reported. In the present study, 82 faecal specimens were collected from 46 giant pandas (Ailuropoda melanoleuca) and 36 red pandas (Ailurus fulgens) in the northwest of China. By PCR and sequencing of the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA) gene of E. bieneusi, an overall infection rate of 10.98% (9/82) was observed in pandas, with 8.70% (4/46) for giant pandas, and 13.89% (5/36) for red pandas. Two ITS genotypes were identified: the novel genotype I-like (n=4) and genotype EbpC (n=5). Multilocus sequence typing (MLST) employing three microsatellites (MS1, MS3 and MS7) and one minisatellite (MS4) showed that nine, six, six and nine positive products were amplified and sequenced successfully at four respective loci. A phylogenetic analysis based on a neighbor-joining tree of the ITS gene sequences of E. bieneusi indicated that the genotype EbpC fell into 1d of group 1 of zoonotic potential, and the novel genotype I-like was clustered into group 2. The present study firstly indicated the presence of E. bieneusi in giant and red pandas, and these results suggested that integrated strategies should be implemented to effectively protect pandas and humans from infecting E. bieneusi in China. Copyright © 2015 Elsevier B.V. All rights reserved.

What makes red quasars red?. Observational evidence for dust extinction from line ratio analysis

NASA Astrophysics Data System (ADS)

Kim, Dohyeong; Im, Myungshin

2018-02-01

Red quasars are very red in the optical through near-infrared (NIR) wavelengths, which is possibly due to dust extinction in their host galaxies as expected in a scenario in which red quasars are an intermediate population between merger-driven star-forming galaxies and unobscured type 1 quasars. However, alternative mechanisms also exist to explain their red colors: (i) an intrinsically red continuum; (ii) an unusual high covering factor of the hot dust component, that is, CFHD = LHD/Lbol, where the LHD is the luminosity from the hot dust component and the Lbol is the bolometric luminosity; and (iii) a moderate viewing angle. In order to investigate why red quasars are red, we studied optical and NIR spectra of 20 red quasars at z 0.3 and 0.7, where the usage of the NIR spectra allowed us to look into red quasar properties in ways that are little affected by dust extinction. The Paschen to Balmer line ratios were derived for 13 red quasars and the values were found to be 10 times higher than unobscured type 1 quasars, suggesting a heavy dust extinction with AV > 2.5 mag. Furthermore, the Paschen to Balmer line ratios of red quasars are difficult to explain with plausible physical conditions without adopting the concept of the dust extinction. The CFHD of red quasars are similar to, or marginally higher than, those of unobscured type 1 quasars. The Eddington ratios, computed for 19 out of 20 red quasars, are higher than those of unobscured type 1 quasars (by factors of 3-5), and hence the moderate viewing angle scenario is disfavored. Consequently, these results strongly suggest the dust extinction that is connected to an enhanced nuclear activity as the origin of the red color of red quasars, which is consistent with the merger-driven quasar evolution scenario. Full Table A.1 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/610/A31

Identification and genetic characterization of Sarcocystis arctica and Sarcocystis lutrae in red foxes (Vulpes vulpes) from Baltic States and Spain.

PubMed

Kirillova, Viktorija; Prakas, Petras; Calero-Bernal, Rafael; Gavarāne, Inese; Fernández-García, José Luis; Martínez-González, Manuel; Rudaitytė-Lukošienė, Eglė; Martínez-Estéllez, Miguel Ángel Habela; Butkauskas, Dalius; Kirjušina, Muza

2018-03-12

Typically, carnivores serve as definitive hosts for Sarcocystis spp. parasites; currently, their role as intermediate hosts is being elucidated. The present study aimed to identify and molecularly characterize Sarcocystis cysts detected in striated muscle of red foxes from different populations in Latvia, Lithuania and Spain. Muscle samples from 411 red foxes (Vulpes vulpes) and 269 racoon dogs (Nyctereutes procyonoides) from Latvia, 41 red foxes from Lithuania and 22 red foxes from Spain were examined for the presence of Sarcocystis sarcocysts by light microscopy (LM). Sarcocystis spp. were identified by transmission electron microscopy (TEM) and molecular biology techniques. Sarcocystis cysts were detected in 11/411 (2.7%) Latvian, 3/41 (7.3%) Lithuanian, and 6/22 (27.3%) Spanish red foxes, however, cysts were not observed in the muscles of racoon dogs. Based on LM, TEM, 18S rDNA, 28S rDNA, ITS1, cox1 and rpoB sequences, Sarcocystis arctica and Sarcocystis lutrae cysts were identified in red fox muscles from Latvia and Lithuania, whereas only S. arctica was detected in Spain. The 18S rDNA, 28S rDNA and ITS1 sequences from the 21 isolates of S. arctica from Latvia, Lithuania and Spain were identical. By contrast, two and four haplotypes were determined based on mtDNA cox1 and apicoplast rpoB sequences, respectively. Polymorphisms were not detected between the two isolates of S. lutrae from Latvia and Lithuania. Based on phylogenetic results, S. arctica and S. lutrae were most closely related to Sarcocystis spp. using predatory mammals as intermediate hosts and to Sarcocystis species with a bird-bird life-cycle. Based on current knowledge, the red fox and Arctic fox (Vulpes lagopus) could act as intermediate host for the same two Sarcocystis species. Molecular results suggest the existence of two genetic lineages of S. arctica, and such divergence relies on its geographical distribution but not on their intermediate host species.

Novel multistep BRET-FRET energy transfer using nanoconjugates of firefly proteins, quantum dots, and red fluorescent proteins

NASA Astrophysics Data System (ADS)

Alam, Rabeka; Zylstra, Joshua; Fontaine, Danielle M.; Branchini, Bruce R.; Maye, Mathew M.

2013-05-01

Sequential bioluminescence resonance energy transfer (BRET) and fluorescence resonance energy transfer (FRET) from firefly luciferase to red fluorescent proteins using quantum dot or rod acceptor/donor linkers is described. The effect of morphology and tuned optical properties on the efficiency of this unique BRET-FRET system was evaluated.Sequential bioluminescence resonance energy transfer (BRET) and fluorescence resonance energy transfer (FRET) from firefly luciferase to red fluorescent proteins using quantum dot or rod acceptor/donor linkers is described. The effect of morphology and tuned optical properties on the efficiency of this unique BRET-FRET system was evaluated. Electronic supplementary information (ESI) available: Experimental details, Fig. S1 and Table S1-S4. See DOI: 10.1039/c3nr01842c

Optically intraconnected computer employing dynamically reconfigurable holographic optical element

NASA Technical Reports Server (NTRS)

Bergman, Larry A. (Inventor)

1992-01-01

An optically intraconnected computer and a reconfigurable holographic optical element employed therein. The basic computer comprises a memory for holding a sequence of instructions to be executed; logic for accessing the instructions in sequence; logic for determining for each the instruction the function to be performed and the effective address thereof; a plurality of individual elements on a common support substrate optimized to perform certain logical sequences employed in executing the instructions; and, element selection logic connected to the logic determining the function to be performed for each the instruction for determining the class of each function and for causing the instruction to be executed by those the elements which perform those associated the logical sequences affecting the instruction execution in an optimum manner. In the optically intraconnected version, the element selection logic is adapted for transmitting and switching signals to the elements optically.

Optical fibre PH sensor based on immobilized indicator

NASA Astrophysics Data System (ADS)

Cai, Defu; Cao, Qiang; Han, JingHong; Cai, Jine; Li, YaTing; Zhu, ZeMin; Fan, Jie; Gao, Ning

1991-08-01

An optical fiber pH sensor which has the immobilized pH sensitive indicator dye reagents on the tip of the optical fiber has been studied. The probe is made by covalently immobilizing the phenol red, bromine phenol blue, or bromothymol blue on the polyacrylamide microsphere fixed by polyterafluoroethylene (PTFE) film. A gap between the dye and optical fiber was used to make the diffusion of the hydrogen ions easier. The parameters of the optical fiber pH sensor have been given completely. The ranges of measurement are 3.0 - 5.0 pH, 7.0 - 8.5 pH, and 8.0 - 10.0 pH for bromine phenol blue, phenol red, and bromothymol blue, respectively. The sensitivity is 66.6 mV/pH. The probe has a precision of better than 0.55 pH. The linear correlation coefficient is 0.999. The response time is 1 - 2 min. The hysteresis is 0.52%. The repeatability is 0.013 mV, while the stability is 0.015 pH/h.

An organic dye-polymer (phenol red-poly (vinyl alcohol)) composite architecture towards tunable -optical and -saturable absorption characteristics

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

Sreedhar, Sreeja, E-mail: sreejasreedhar83@gmail.com; Muneera, C. I., E-mail: drcimuneera@hotmail.com; Illyaskutty, Navas

2016-05-21

Herein, we demonstrate that blending an organic dye (guest/filler), with a vinyl polymer (host template), is an inexpensive and simple approach for the fabrication of multifunctional photonic materials which could display an enhancement in the desirable properties of the constituent materials and, at the same time provide novel synergistic properties for the guest-host system. A new guest-host nanocomposite system comprising Phenol Red dye and poly (vinyl alcohol) as guest and host template, respectively, which exhibits tunable optical characteristics and saturable absorption behavior, is introduced. The dependence of local electronic environment provided by the polymer template and the interactions of themore » polymer molecules with the encapsulated guest molecules on the observed optical/nonlinear absorption behavior is discussed. An understanding of the tunability of the optical/ photophysical processes, with respect to the filler content, as discussed herein could help in the design of improved optical materials for several photonic device applications like organic light emitting diodes and saturable absorbers.« less

A symmetric bipolar nebula around MWC 922.

PubMed

Tuthill, P G; Lloyd, J P

2007-04-13

We report regular and symmetric structure around dust-enshrouded Be star MWC 922 obtained with infrared imaging. Biconical lobes that appear nearly square in aspect, forming this "Red Square" nebula, are crossed by a series of rungs that terminate in bright knots or "vortices," and an equatorial dark band crossing the core delimits twin hyperbolic arcs. The intricate yet cleanly constructed forms that comprise the skeleton of the object argue for minimal perturbation from global turbulent or chaotic effects. We also report the presence of a linear comb structure, which may arise from optically projected shadows of a periodic feature in the inner regions, such as corrugations in the rim of a circumstellar disk. The sequence of nested polar rings draws comparison with the triple-ring system seen around the only naked-eye supernova in recent history: SN1987A.

The Optical Gravitational Lensing Experiment. Small Amplitude Variable Red Giants in the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Soszynski, I.; Udalski, A.; Kubiak, M.; Szymanski, M.; Pietrzynski, G.; Zebrun, K.; Szewczyk, O.; Wyrzykowski, L.

2004-06-01

We present analysis of the large sample of variable red giants from the Large and Small Magellanic Clouds detected during the second phase of the Optical Gravitational Lensing Experiment (OGLE-II) and supplemented with OGLE-III photometry. Comparing pulsation properties of detected objects we find that they constitute two groups with clearly distinct features. In this paper we analyze in detail small amplitude variable red giants (about 15400 and 3000 objects in the LMC and SMC, respectively). The vast majority of these objects are multi-periodic. At least 30% of them exhibit two modes closely spaced in the power spectrum, what likely indicates non-radial oscillations. About 50% exhibit additional so called Long Secondary Period. To distinguish between AGB and RGB red giants we compare PL diagrams of multi-periodic red giants located above and below the tip of the Red Giant Branch (TRGB). The giants above the TRGB form four parallel ridges in the PL diagram. Among much more numerous sample of giants below the TRGB we find objects located on the low luminosity extensions of these ridges, but most of the stars are located on the ridges slightly shifted in log P. We interpret the former as the second ascent AGB red giants and the latter as the first ascent RGB objects. Thus, we empirically show that the pulsating red giants fainter than the TRGB are a mixture of RGB and AGB giants. Finally, we compare the Petersen diagrams of the LMC, SMC and Galactic bulge variable red giants and find that they are basically identical indicating that the variable red giants in all these different stellar environments share similar pulsation properties.

Sarcocystis spp. Infection in two Red Panda Cubs (Ailurus fulgens).

PubMed

Zoll, W M; Needle, D B; French, S J; Lim, A; Bolin, S; Langohr, I; Agnew, D

2015-01-01

Two neonatal male red panda (Ailurus fulgens) littermates were submitted for necropsy examination. One animal was found dead with no prior signs of illness; the other had a brief history of laboured breathing. Post-mortem examination revealed disseminated protozoal infection. To further characterize the causative agent, transmission electron microscopy (TEM), immunohistochemistry (IHC), polymerase chain reaction (PCR) and amplification and nucleic acid sequencing were performed. IHC was negative for Toxoplasma gondii and Neospora caninum, but was positive for a Sarcocystis spp. TEM of cardiac muscle and lung revealed numerous intracellular apicomplexan protozoa within parasitophorous vacuoles. PCR and nucleic acid sequencing of partial 18S rRNA and the internal transcribed spacer (ITS)-1 region confirmed a Sarcocystis spp. that shared 99% sequence homology to Sarcocystis neurona and Sarcocystis dasypi. This represents the first report of sarcocystosis in red pandas. The histopathological, immunohistochemical, molecular and ultrastructural findings are supportive of vertical transmission resulting in fatal disseminated disease. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Effects of light quality on the growth characteristics and biochemical component of Chlorella pyrenoidosa].

PubMed

Tang, Qing-Qing; Fang, Zhi-Guo; Ji, Wen-Wen; Xia, Hui-Long

2014-11-01

Effect of light quality, including red light, blue light, white light, red and blue mixing light with ratios of 8: 1, 8:2 and 8 : 3, on the growth characteristics and biochenmical composition of Chlorella pyrenoidosa was investigated based on light emitting diode (LED). Results showed that Chlorella pyrenoidosa grew best under blue light, and the optical density, specific growth rate and biomass of Chlorella pyrenoidosa was about 2.4, 0.10 d(-1) and 0.64 g x L(-1), respectively, while the optical density of Chlorella pyrenoidosa was between 1.0 and 1.7, the specific growth rate was between 0.07-0.10 d(-1) and the biomass was between 0.27 and 0.38 g x L(-1) under other light quality after 30 days of cultivation. Under blue light, the optical density, specific growth rate and biomass of Chlorella pyrenoidosa was approximately 2.05 times, 1.33 times and 2.06 times higher than red light, respectively. Moreover, red and blue mixing light was conducive to the synthesis of chlorophyll a and β-carotene of Chlorella pyrenoidosa, and blue light could promote the synthesis of chlorophyll b. Chlorophyll a and carotenoids content of Chlorella pyrenoidosa was 13.5 mg xg(-1) and 5.8 mg x g(-1) respectively under red and blue mixing light with a ratio of 8:1, while it was 8.4 mg x g(-1) and 3.6 mg x g(-1) respectively under blue light. Red and blue mixing light was more conducive to protein and total lipid content per dry cell of Chlorella pyrenoidosa. Protein and total lipid content was 489.3 mg x g(-1) and 311.2 mg x g(-1) under red and blue mixing light with a ratio of 8 : 3, while it was 400.9 mg x g(-1) and 231.9 mg x g(-1) respectively under blue light.

A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.).

PubMed

Baldwin, Samantha; Revanna, Roopashree; Thomson, Susan; Pither-Joyce, Meeghan; Wright, Kathryn; Crowhurst, Ross; Fiers, Mark; Chen, Leshi; Macknight, Richard; McCallum, John A

2012-11-19

Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers. We report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line 'CUDH2150' and the genetically distant Indian landrace 'Nasik Red', using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of 'Nasik Red' reads onto 'CUDH2150' assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F(2) progeny from a very large F(2) family developed from the 'Nasik Red' x 'CUDH2150' inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis. The generic tools developed for the Galaxy environment enable rapid development of sets of PCR assays targeting sequence variants identified from Illumina and 454 sequence data. They enable non-specialist users to validate and exploit large volumes of next-generation sequence data using basic equipment.

Systemic AA amyloidosis in the red fox (Vulpes vulpes).

PubMed

Rising, Anna; Cederlund, Ella; Palmberg, Carina; Uhlhorn, Henrik; Gaunitz, Stefan; Nordling, Kerstin; Ågren, Erik; Ihse, Elisabet; Westermark, Gunilla T; Tjernberg, Lars; Jörnvall, Hans; Johansson, Jan; Westermark, Per

2017-11-01

Amyloid A (AA) amyloidosis occurs spontaneously in many mammals and birds, but the prevalence varies considerably among different species, and even among subgroups of the same species. The Blue fox and the Gray fox seem to be resistant to the development of AA amyloidosis, while Island foxes have a high prevalence of the disease. Herein, we report on the identification of AA amyloidosis in the Red fox (Vulpes vulpes). Edman degradation and tandem MS analysis of proteolyzed amyloid protein revealed that the amyloid partly was composed of full-length SAA. Its amino acid sequence was determined and found to consist of 111 amino acid residues. Based on inter-species sequence comparisons we found four residue exchanges (Ser31, Lys63, Leu71, Lys72) between the Red and Blue fox SAAs. Lys63 seems unique to the Red fox SAA. We found no obvious explanation to how these exchanges might correlate with the reported differences in SAA amyloidogenicity. Furthermore, in contrast to fibrils from many other mammalian species, the isolated amyloid fibrils from Red fox did not seed AA amyloidosis in a mouse model. © 2017 The Protein Society.

Optical measurements of lung microvascular filtration coefficient using polysulfone fibers.

PubMed

Klaesner, J W; Roselli, R J; Evans, S; Pou, N A; Parker, R E; Tack, G; Parham, M

1994-01-01

Lung fluid balance, which is governed by the product of net transvascular pressure difference and lung filtration coefficient, can be altered in pulmonary diseases. A simple measurement of the lung filtration coefficient (Kfc) would be clinically useful and has been examined by several researchers. Current methods of determining Kfc include gravimetric measurement in isolated lungs and lymph node cannulation, neither of which can be extended to human use. Optical measurements of protein concentration changes in venous blood can be combined with pressure measurements to calculate Kfc. Blood, though, contains red corpuscles, which tend to absorb and scatter light, obscuring these optical measurements. In this study, an optical system was developed in which a polysulfone filter cartridge was used to remove red blood cells before the filtrate was passed through a spectrophotometer. Absorbance changes caused by changes in concentration of albumin labeled with Evans Blue were monitored at 620 nm after venous pressure was elevated by about 13 cm H2O. Optical measurements of Kfc averaged 0.401 +/- 0.074 (ml/min cm H2O 100 g DLW) for an isolated canine lung. Optical measurements of Kfc (0.363 +/- 0.120 ml/min cm H2O 100 g DLW) were made for the first time in an intact, closed chest sheep in which pulmonary pressure was altered by inflating a Foley balloon in the left atrium. We conclude that absorbance and scattering artifacts introduced by red blood cells can be eliminated by first filtering the blood through polysulfone fibers. Kfc measurements using the optical method are similar to values obtained by others using gravimetric methods. Finally, we have demonstrated that the technique can be used to estimate Kfc in an intact animal.

High sensitivity radiochromic film dosimetry using an optical common-mode rejection and a reflective-mode flatbed color scanner.

PubMed

Ohuchi, Hiroko

2007-11-01

A novel method that can greatly improve the dosimetric sensitivity limit of a radiochromic film (RCF) through use of a set of color components, e.g., red and green, outputs from a RGB color scanner has been developed. RCFs are known to have microscopic and macroscopic nonuniformities, which come from the thickness variations in the film's active radiochromic layer and coating. These variations in the response make the optical signal-to-noise ratio lower, resulting in lower film sensitivity. To mitigate the effects of RCF nonuniform response, an optical common-mode rejection (CMR) was developed. The CMR compensates nonuniform response by creating a ratio of the two signals where the factors common to both numerator and denominator cancel out. The CMR scheme was applied to the mathematical operation of creating a ratio using two components, red and green outputs from a scanner. The two light component lights are neighboring wavebands about 100 nm apart and suffer a common fate, with the exception of wavelength-dependent events, having passed together along common attenuation paths. Two types of dose-response curves as a function of delivered dose ranging from 3.7 mGy to 8.1 Gy for 100 kV x-ray beams were obtained with the optical CMR scheme and the conventional analysis method using red component, respectively. In the range of 3.7 mGy to 81 mGy, the optical densities obtained with the optical CMR showed a good consistency among eight measured samples and an improved consistency with a linear fit within 1 standard deviation of each measured optical densities, while those with the conventional analysis exhibited a large discrepancy among eight samples and did not show a consistency with a linear fit.

Test Input Generation for Red-Black Trees using Abstraction

NASA Technical Reports Server (NTRS)

Visser, Willem; Pasareanu, Corina S.; Pelanek, Radek

2005-01-01

We consider the problem of test input generation for code that manipulates complex data structures. Test inputs are sequences of method calls from the data structure interface. We describe test input generation techniques that rely on state matching to avoid generation of redundant tests. Exhaustive techniques use explicit state model checking to explore all the possible test sequences up to predefined input sizes. Lossy techniques rely on abstraction mappings to compute and store abstract versions of the concrete states; they explore under-approximations of all the possible test sequences. We have implemented the techniques on top of the Java PathFinder model checker and we evaluate them using a Java implementation of red-black trees.

TSCA Environmental Release Application (TERA) for Alcaligenes xylosoxidans subspecies denitrificans strain AL6.1

EPA Pesticide Factsheets

TERA submitted by University of California, Riverside and given the tracking designation of R-03-0001. The microorganism has been modified to carry a coding sequence of DsRed for expressing a red fluorescent protein.

Spectroscopic Confirmation of a Massive Red-sequence Selected Galaxy Cluster at Z=1.34 in the SpARCS-South Cluster Survey

NASA Technical Reports Server (NTRS)

Wilson, Gillian; Demarco, Ricardo; Muzzin, Adam; Yee, H.K.C.; Lacy, Mark; Surace, Jason; Gilbank, David; Blindert, Kris; Hoekstra, Henk; Majumdar, Subhabrata;

Integration of Next Generation Sequencing and EPR Analysis to Uncover Molecular Mechanism Underlying Shell Color Variation in Scallops

PubMed Central

Sun, Xiujun; Liu, Zhihong; Zhou, Liqing; Wu, Biao; Dong, Yinghui; Yang, Aiguo

2016-01-01

The Yesso scallop Patinopecten yessoensis displays polymorphism in shell colors, which is of great interest for the scallop industry. To identify genes involved in the shell coloration, in the present study, we investigate the transcriptome differences by Illumina digital gene expression (DGE) analysis in two extreme color phenotypes, Red and White. Illumina sequencing yields a total of 62,715,364 clean sequence reads, and more than 85% reads are mapped into our previously sequenced transcriptome. There are 25 significantly differentially expressed genes between Red and White scallops. EPR (Electron paramagnetic resonance) analysis has identified EPR spectra of pheomelanin and eumelanin in the red shells, but not in the white shells. Compared to the Red scallops, the White scallops have relatively higher mRNA expression in tyrosinase genes, but lower expression in other melanogensis-associated genes. Meantime, the relatively lower tyrosinase protein and decreased tyrosinase activity in White scallops are suggested to be associated with the lack of melanin in the white shells. Our findings highlight the functional roles of melanogensis-associated genes in the melanization process of scallop shells, and shed new lights on the transcriptional and post-transcriptional mechanisms in the regulation of tyrosinase activity during the process of melanin synthesis. The present results will assist our molecular understanding of melanin synthesis underlying shell color polymorphism in scallops, as well as other bivalves, and also help the color-based breeding in shellfish aquaculture. PMID:27563719

The optical effect of a semiconductor laser on protecting wheat from UV-B radiation damage.

PubMed

Qiu, Zong-Bo; Zhu, Xin-Jun; Li, Fang-Min; Liu, Xiao; Yue, Ming

2007-07-01

Lasers have been widely used in the field of biology along with the development of laser technology, but the mechanism of the bio-effect of lasers is not explicit. The objective of this paper was to test the optical effect of a laser on protecting wheat from UV-B damage. A patent instrument was employed to emit semiconductor laser (wavelength 650 nm) and incoherent red light, which was transformed from the semiconductor laser. The wavelength, power and lightfleck diameter of the incoherent red light are the same as those of the semiconductor laser. The semiconductor laser (wavelength 650 nm, power density 3.97 mW mm(-2)) and incoherent red light (wavelength 650 nm, power density 3.97 mW mm(-2)) directly irradiated the embryo of wheat seeds for 3 min respectively, and when the seedlings were 12-day-old they were irradiated by UV-B radiation (10.08 kJ m(-2)) for 12 h in the dark. Changes in the concentration of malondialdehyde (MDA), hydrogen peroxide (H(2)O(2)), glutathione (GSH), ascorbate (AsA), carotenoids (CAR), the production rate of superoxide radical (O(2)(-)), the activities of peroxidase (POD), catalase (CAT), superoxide dismutase (SOD) and the growth parameters of seedlings (plant height, leaf area and fresh weight) were measured to test the optical effect of the laser. The results showed that the incoherent red light treatment could not enhance the activities of SOD, POD and CAT and the concentration of AsA and CAR. When the plant cells were irradiated by UV-B, the incoherent red light treatment could not eliminate active oxygen and prevent lipid peroxidation in wheat. The results also clearly demonstrate that the plant DNA was damaged by UV-B radiation and semiconductor laser irradiance had the capability to protect plants from UV-B-induced DNA damage, while the incoherent red light could not. This is the first investigation reporting the optical effect of a semiconductor laser on protecting wheat from UV-B radiation damage.

INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles

PubMed Central

Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B.

2013-01-01

Background The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. Results We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. Conclusions We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo. PMID:24324765

INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

PubMed

Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba Alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B

2013-01-01

The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

A Leafhopper-Transmissible DNA Virus with Novel Evolutionary Lineage in the Family Geminiviridae Implicated in Grapevine Redleaf Disease by Next-Generation Sequencing

PubMed Central

Poojari, Sudarsana; Alabi, Olufemi J.; Fofanov, Viacheslav Y.; Naidu, Rayapati A.

2013-01-01

A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging disease, designated as grapevine redleaf disease (GRD). High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV), and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh) from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms. PMID:23755117

The optical depth sensor (ODS) for column dust opacity measurements and cloud detection on martian atmosphere

NASA Astrophysics Data System (ADS)

Toledo, D.; Rannou, P.; Pommereau, J.-P.; Foujols, T.

2016-08-01

A lightweight and sophisticated optical depth sensor (ODS) able to measure alternatively scattered flux at zenith and the sum of the direct flux and the scattered flux in blue and red has been developed to work in martian environment. The principal goals of ODS are to perform measurements of the daily mean dust opacity and to retrieve the altitude and optical depth of high altitude clouds at twilight, crucial parameters in the understanding of martian meteorology. The retrieval procedure of dust opacity is based on the use of radiative transfer simulations reproducing observed changes in the solar flux during the day as a function of 4 free parameters: dust opacity in blue and red, and effective radius and effective width of dust size distribution. The detection of clouds is undertaken by looking at the time variation of the color index (CI), defined as the ratio between red and blue ODS channels, at twilight. The retrieval of altitude and optical depth of clouds is carried out using a radiative transfer model in spherical geometry to simulate the CI time variation at twilight. Here the different retrieval procedures to analyze ODS signals, as well as the results obtained in different sensitivity analysis are presented and discussed.

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

NASA Astrophysics Data System (ADS)

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

2008-02-01

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

Phylogeny of geminivirus coat protein sequences and digital PCR aid in identifying Spissistilus festinus (Say) as a vector of Grapevine red blotch-associated virus

USDA-ARS?s Scientific Manuscript database

Grapevine red blotch-associated virus (GRBaV) is a newly identified virus of grapevines, and a putative member of a new genus within the family Geminiviridae. This virus is associated with red blotch disease that was first reported in California in 2008. It affects the profitability of vineyards by ...

Pressure injury prediction using diffusely scattered light

NASA Astrophysics Data System (ADS)

Diaz, David; Lafontant, Alec; Neidrauer, Michael; Weingarten, Michael S.; DiMaria-Ghalili, Rose Ann; Scruggs, Ericka; Rece, Julianne; Fried, Guy W.; Kuzmin, Vladimir L.; Zubkov, Leonid

2017-02-01

Pressure injuries (PIs) originate beneath the surface of the skin at the interface between bone and soft tissue. We used diffuse correlation spectroscopy (DCS) and diffuse near-infrared spectroscopy (DNIRS) to predict the development of PIs by measuring dermal and subcutaneous red cell motion and optical absorption and scattering properties in 11 spinal cord injury subjects with only nonbleachable redness in the sacrococcygeal area in a rehabilitation hospital and 20 healthy volunteers. A custom optical probe was developed to obtain continuous DCS and DNIRS data from sacrococcygeal tissue while the subjects were placed in supine and lateral positions to apply pressure from body weight and to release pressure, respectively. Rehabilitation patients were measured up to four times over a two-week period. Three rehabilitation patients developed open PIs (POs) within four weeks and eight patients did not (PNOs). Temporal correlation functions in the area of redness were significantly different (p<0.01) during both baseline and applied pressure stages for POs and PNOs. The results show that our optical method may be used for the early prediction of ulcer progression.

Pavement marking visibility requirements during wet night conditions.

DOT National Transportation Integrated Search

2006-01-01

This study investigated the performance of pavement markings in wet night conditions. Typically, performance will decrease in wet conditions. The degradation is a result of flooding of the marking optics and a change in the optical media, thereby red...

High power diode lasers emitting from 639 nm to 690 nm

NASA Astrophysics Data System (ADS)

Bao, L.; Grimshaw, M.; DeVito, M.; Kanskar, M.; Dong, W.; Guan, X.; Zhang, S.; Patterson, J.; Dickerson, P.; Kennedy, K.; Li, S.; Haden, J.; Martinsen, R.

2014-03-01

There is increasing market demand for high power reliable red lasers for display and cinema applications. Due to the fundamental material system limit at this wavelength range, red diode lasers have lower efficiency and are more temperature sensitive, compared to 790-980 nm diode lasers. In terms of reliability, red lasers are also more sensitive to catastrophic optical mirror damage (COMD) due to the higher photon energy. Thus developing higher power-reliable red lasers is very challenging. This paper will present nLIGHT's released red products from 639 nm to 690nm, with established high performance and long-term reliability. These single emitter diode lasers can work as stand-alone singleemitter units or efficiently integrate into our compact, passively-cooled Pearl™ fiber-coupled module architectures for higher output power and improved reliability. In order to further improve power and reliability, new chip optimizations have been focused on improving epitaxial design/growth, chip configuration/processing and optical facet passivation. Initial optimization has demonstrated promising results for 639 nm diode lasers to be reliably rated at 1.5 W and 690nm diode lasers to be reliably rated at 4.0 W. Accelerated life-test has started and further design optimization are underway.

Kepler-432 b: a massive warm Jupiter in a 52-day eccentric orbit transiting a giant star

NASA Astrophysics Data System (ADS)

Ortiz, Mauricio; Gandolfi, Davide; Reffert, Sabine; Quirrenbach, Andreas; Deeg, Hans J.; Karjalainen, Raine; Montañés-Rodríguez, Pilar; Nespral, David; Nowak, Grzegorz; Osorio, Yeisson; Palle, Enric

2015-01-01

We study the Kepler object Kepler-432, an evolved star ascending the red giant branch. By deriving precise radial velocities from multi-epoch high-resolution spectra of Kepler-432 taken with the CAFE spectrograph at the 2.2 m telescope of Calar Alto Observatory and the FIES spectrograph at the Nordic Optical Telescope of Roque de Los Muchachos Observatory, we confirm the planetary nature of the object Kepler-432 b, which has a transit period of 52 days. We find a planetary mass of Mp = 5.84 ± 0.05MJup and a high eccentricity of e = 0.478 ± 0.004. With a semi-major axis of a = 0.303 ± 0.007 AU, Kepler-432 b is the first bona fide warm Jupiter detected to transit a giant star. We also find a radial velocity linear trend of γ˙ = 0.44 ± 0.04 m s-1 d-1, which suggests the presence of a third object in the system. Current models of planetary evolution in the post-main-sequence phase predict that Kepler-432 b will be most likely engulfed by its host star before the latter reaches the tip of the red giant branch. Based on observations collected at the German-Spanish Astronomical Center, Calar Alto, jointly operated by the Max-Planck-Institut für Astronomie (Heidelberg) and the Instituto de Astrofísica de Andalucía (IAA-CSIC, Granada).Based on observations obtained with the Nordic Optical Telescope, operated on the island of La Palma jointly by Denmark, Finland, Iceland, Norway, and Sweden, in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofísica de Canarias.Table 3 is available in electronic form at http://www.aanda.org

Atom guidance in the TE01 donut mode of a large-core hollow fiber

NASA Astrophysics Data System (ADS)

Pechkis, J. A.; Fatemi, F. K.

2011-05-01

We report on our progress towards low-light-level nonlinear optics experiments by optically guiding atoms in the TE01 donut mode of a hollow fiber. Atoms are transported over 12 cm from a ``source'' magneto-optical trap (MOT) through a 100- μm-diameter hollow fiber and are recaptured by a ``collection'' MOT situated directly below the fiber. For red-detuned guiding, we compare the guiding efficiency between the fundamental (Gaussian-like) mode and this donut mode, which has a larger guiding area but lower peak intensity. We also discuss our progress in transporting atoms in the dark core of this mode using blue-detuned light, which has more stringent constraints to atom guidance compared to red-detuned light. This work is supported by ONR.

Tungsten-incorporation induced red-shift in the bandgap of gallium oxide thin films

NASA Astrophysics Data System (ADS)

Rubio, E. J.; Ramana, C. V.

2013-05-01

Tungsten (W) incorporated Ga2O3 films were produced by co-sputter deposition. W-concentration was varied by the applied sputtering-power. The structure and optical properties of W-incorporated Ga2O3 films were evaluated using X-ray diffraction, scanning electron microscopy, and spectrophotometric measurements. No secondary phase formation was observed in W-incorporated Ga2O3 films. W-induced effects were significant on the structure and optical properties of Ga2O3 films. The bandgap of Ga2O3 films without W-incorporation was ˜5 eV. Red-shift in the bandgap was noted with increasing W-concentration indicating the electronic structure changes in W-Ga2O3 films. A functional relationship between W-concentration and optical property is discussed.

Melanocortin 1 receptor (MC1R) gene sequence variation and melanism in the gray (Sciurus carolinensis), fox (Sciurus niger), and red (Sciurus vulgaris) squirrel.

PubMed

McRobie, Helen R; King, Linda M; Fanutti, Cristina; Coussons, Peter J; Moncrief, Nancy D; Thomas, Alison P M

2014-01-01

Sequence variations in the melanocortin 1 receptor (MC1R) gene are associated with melanism in many different species of mammals, birds, and reptiles. The gray squirrel (Sciurus carolinensis), found in the British Isles, was introduced from North America in the late 19th century. Melanism in the British gray squirrel is associated with a 24-bp deletion in the MC1R. To investigate the origin of this mutation, we sequenced the MC1R of 95 individuals including 44 melanic gray squirrels from both the British Isles and North America. Melanic gray squirrels of both populations had the same 24-bp deletion associated with melanism. Given the significant deletion associated with melanism in the gray squirrel, we sequenced the MC1R of both wild-type and melanic fox squirrels (Sciurus niger) (9 individuals) and red squirrels (Sciurus vulgaris) (39 individuals). Unlike the gray squirrel, no association between sequence variation in the MC1R and melanism was found in these 2 species. We conclude that the melanic gray squirrel found in the British Isles originated from one or more introductions of melanic gray squirrels from North America. We also conclude that variations in the MC1R are not associated with melanism in the fox and red squirrels.

Molecular epidemiological characterization of poultry red mite, Dermanyssus gallinae, in Japan

PubMed Central

CHU, Thi Thanh Huong; MURANO, Takako; UNO, Yukiko; USUI, Tatsufumi; YAMAGUCHI, Tsuyoshi

2015-01-01

Dermanyssus gallinae, the poultry red mite, is an obligatory blood-sucking ectoparasite. The genetic diversity of D. gallinae has been examined in some countries, but so far not in Asian countries. Here, we sequenced a part of the mitochondrial cytochrome oxidase subunit I (COI) and16S rRNA genes and nuclear internal transcribed spacers (ITS) region in 239 mite samples collected from 40 prefectures throughout Japan. The COI and 16S rRNA nucleotide sequences were classified into 28 and 26 haplotypes, respectively. In phylogenetic trees, the haplotypes clustered into 2 haplogroups corresponding to haplogroups A and B, which were previously reported. Haplogroups A and B were further subdivided into sub-haplogroups AJ1 and AJ2, and BJ1 and BJ2, respectively. In both trees, the sequences of haplotypes in AJ1 and BJ2 were relatively distant from those reported in other countries, while some sequences in AJ2 and BJ1 were identical to those in Europe. In addition, the ITS sequences were classified into two sequences, and both sequences were closely related to the sequences found in European countries. These findings indicate a possibility of international oversea transmission of D. gallinae. PMID:26074251

Molecular epidemiological characterization of poultry red mite, Dermanyssus gallinae, in Japan.

PubMed

Chu, Thi Thanh Huong; Murano, Takako; Uno, Yukiko; Usui, Tatsufumi; Yamaguchi, Tsuyoshi

2015-11-01

Dermanyssus gallinae, the poultry red mite, is an obligatory blood-sucking ectoparasite. The genetic diversity of D. gallinae has been examined in some countries, but so far not in Asian countries. Here, we sequenced a part of the mitochondrial cytochrome oxidase subunit I (COI) and16S rRNA genes and nuclear internal transcribed spacers (ITS) region in 239 mite samples collected from 40 prefectures throughout Japan. The COI and 16S rRNA nucleotide sequences were classified into 28 and 26 haplotypes, respectively. In phylogenetic trees, the haplotypes clustered into 2 haplogroups corresponding to haplogroups A and B, which were previously reported. Haplogroups A and B were further subdivided into sub-haplogroups AJ1 and AJ2, and BJ1 and BJ2, respectively. In both trees, the sequences of haplotypes in AJ1 and BJ2 were relatively distant from those reported in other countries, while some sequences in AJ2 and BJ1 were identical to those in Europe. In addition, the ITS sequences were classified into two sequences, and both sequences were closely related to the sequences found in European countries. These findings indicate a possibility of international oversea transmission of D. gallinae.

Rapid detection and differentiation of Staphylococcus colonies using an optical scattering technology.

PubMed

Alsulami, Tawfiq S; Zhu, Xingyue; Abdelhaseib, Maha Usama; Singh, Atul K; Bhunia, Arun K

2018-05-24

Staphylococcus species are a major pathogen responsible for nosocomial infections and foodborne illnesses. We applied a laser-based BARDOT (bacterial rapid detection using optical scattering technology) for rapid colony screening and detection of Staphylococcus on an agar plate and differentiate these from non-Staphylococcus spp. Among the six growth media tested, phenol red mannitol agar (PRMA) was found most suitable for building the Staphylococcus species scatter image libraries. Scatter image library for Staphylococcus species gave a high positive predictive value (PPV 87.5-100%) when tested against known laboratory strains of Staphylococcus spp., while the PPV against non-Staphylococcus spp. was 0-38%. A total of nine naturally contaminated bovine raw milk and ready-to-eat chicken salad samples were tested, and BARDOT detected Staphylococcus including Staphylococcus aureus with 80-100% PPV. Forty-five BARDOT-identified bacterial isolates from naturally contaminated foods were further confirmed by tuf and nuc gene-specific PCR and 16S rRNA gene sequence. This label-free, non-invasive on-plate colony screening technology can be adopted by the food industries, biotechnology companies, and public health laboratories for Staphylococcus species detection including S. aureus from various samples for food safety and public health management. Graphical abstract.

An intermediate luminosity optical transient (ILOTs) model for the young stellar object ASASSN-15qi

NASA Astrophysics Data System (ADS)

Kashi, Amit; Soker, Noam

2017-07-01

We construct a scenario where the outburst of the young stellar object ASASSN-15qi is an intermediate luminosity optical transient (ILOT). In this scenario, a sub-Jupiter young planet was tidally destructed on to a young main-sequence (MS) star. The system is young, and therefore the radius of the planet is larger than its final value; consequently, its density is smaller. The lower density allows the tidal destruction of the young Saturn-like planet on to the MS star of mass ≈2.4 M⊙, resulting in the formation of a disc and a gravitationally powered ILOT. Unlike the case of the more energetic ILOT V838 Mon, the mass of the destructed planet is too low to inflate a giant envelope, and hence the merger remnant remains hot. If our suggested model holds, this ILOT possesses two interesting properties: (I) its luminosity and total energy are below those of novae; (II) it is not as red as other ILOTs. The unusual outburst of ASASSN-15qi - if indeed is an ILOT - further increases the diversity of the already heterogeneous group of ILOTs. We mark the region on the energy-time diagram occupied by such young ILOTs.

Diversity of the TLR4 Immunity Receptor in Czech Native Cattle Breeds Revealed Using the Pacific Biosciences Sequencing Platform.

PubMed

Novák, Karel; Pikousová, Jitka; Czerneková, Vladimíra; Mátlová, Věra

2017-07-03

The allelic variants of immunity genes in historical breeds likely reflect local infection pressure and therefore represent a reservoir for breeding. Screening to determine the diversity of the Toll-like receptor gene TLR4 was conducted in two conserved cattle breeds: Czech Red and Czech Red Pied. High-throughput sequencing of pooled PCR amplicons using the PacBio platform revealed polymorphisms, which were subsequently confirmed via genotyping techniques. Eight SNPs found in coding and adjacent regions were grouped into 18 haplotypes, representing a significant portion of the known diversity in the global breed panel and presumably exceeding diversity in production populations. Notably, the ancient Czech Red breed appeared to possess greater haplotype diversity than the Czech Red Pied breed, a Simmental variant, although the haplotype frequencies might have been distorted by significant crossbreeding and bottlenecks in the history of Czech Red cattle. The differences in haplotype frequencies validated the phenotypic distinctness of the local breeds. Due to the availability of Czech Red Pied production herds, the effect of intensive breeding on TLR diversity can be evaluated in this model. The advantages of the Pacific Biosciences technology for the resequencing of long PCR fragments with subsequent direct phasing were independently validated.

Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Red Tilapia.

PubMed

Zhu, Wenbin; Wang, Lanmei; Dong, Zaijie; Chen, Xingting; Song, Feibiao; Liu, Nian; Yang, Hui; Fu, Jianjun

2016-08-11

Red tilapia is becoming more popular for aquaculture production in China in recent years. However, the pigmentation differentiation in genetic breeding is the main problem limiting its development of commercial red tilapia culture and the genetic basis of skin color variation is still unknown. In this study, we conducted Illumina sequencing of transcriptome on three color variety red tilapia. A total of 224,895,758 reads were generated, resulting in 160,762 assembled contigs that were used as reference contigs. The contigs of red tilapia transcriptome had hits in the range of 53.4% to 86.7% of the unique proteins of zebrafish, fugu, medaka, three-spined stickleback and tilapia. And 44,723 contigs containing 77,423 simple sequence repeats (SSRs) were identified, with 16,646 contigs containing more than one SSR. Three skin transcriptomes were compared pairwise and the results revealed that there were 148 common significantly differentially expressed unigenes and several key genes related to pigment synthesis, i.e. tyr, tyrp1, silv, sox10, slc24a5, cbs and slc7a11, were included. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in red tilapia and accelerate the molecular selection of the specific strain with consistent skin colors.

Genetic diversity and population history of the red panda (Ailurus fulgens) as inferred from mitochondrial DNA sequence variations.

PubMed

Su, B; Fu, Y; Wang, Y; Jin, L; Chakraborty, R

2001-06-01

The red panda (Ailurus fulgens) is one of the flagship species in worldwide conservation and is of special interest in evolutionary studies due to its taxonomic uniqueness. We sequenced a 236-bp fragment of the mitochondrial D-loop region in a sample of 53 red pandas from two populations in southwestern China. Seventeen polymorphic sites were found, together with a total of 25 haplotypes, indicating a high level of genetic diversity in the red panda. However, no obvious genetic divergence was detected between the Sichuan and Yunnan populations. The consensus phylogenetic tree of the 25 haplotypes was starlike. The pairwise mismatch distribution fitted into a pattern of populations undergoing expansion. Furthermore, Fu's F(S) test of neutrality was significant for the total population (F(S) = -7.573), which also suggests a recent population expansion. Interestingly, the effective population size in the Sichuan population was both larger and more stable than that in the Yunnan population, implying a southward expansion from Sichuan to Yunnan.

GM2-Gangliosidosis, AB Variant: Clinical, Ophthalmological, MRI, and Molecular Findings.

PubMed

Renaud, Deborah; Brodsky, Michael

2016-01-01

GM2-gangliosidosis, AB variant is a very rare form of GM2 gangliosidosis due to a deficiency of GM2 activator protein, associated with autosomal recessive mutations in GM2A. Less than ten patients, confirmed by molecular analysis, have been described in the literature.A 12-month-old Hmong girl presented to the neurometabolic clinic for evaluation of global developmental delay, hypotonia, and cherry red spots. The parents were not known to be consanguineous. Her examination was remarkable for hypotonia with hyperreflexia and excessive startling. The head circumference was normal. An extensive neurometabolic evaluation was negative.Developmental regression began at 14 months of age. Retinal examination at 16 months of age disclosed 4+ cherry red/black spots with "heaped up" ring of whitish infiltrate surrounding both foveae but no evidence of optic atrophy or peripheral retinal abnormalities. Repeat magnetic resonance imaging (MRI) scan at 17 months of age revealed delayed but interval myelination associated with abnormal signal intensity of the bilateral thalami presenting as T2 hyperintensity of the posterior thalami in the region of the pulvinar nuclei and T2 hypointensity in the anterior thalami. Sequencing of the GM2A gene revealed a homozygous c.160 G>T mutation, predicted to result in a premature protein termination p. Glu54*.

Spatially Resolved Spectroscopy of Narrow-line Seyfert 1 Host Galaxies

NASA Astrophysics Data System (ADS)

Scharwächter, J.; Husemann, B.; Busch, G.; Komossa, S.; Dopita, M. A.

2017-10-01

We present optical integral field spectroscopy for five z< 0.062 narrow-line Seyfert 1 (NLS1) galaxies, probing their host galaxies at ≳ 2{--}3 {kpc} scales. Emission lines from the active galactic nucleus (AGN) and the large-scale host galaxy are analyzed separately, based on an AGN-host decomposition technique. The host galaxy gas kinematics indicates large-scale gas rotation in all five sources. At the probed scales of ≳ 2{--}3 {kpc}, the host galaxy gas is found to be predominantly ionized by star formation without any evidence of a strong AGN contribution. None of the five objects shows specific star formation rates (SFRs) exceeding the main sequence of low-redshift star-forming galaxies. The specific SFRs for MCG-05-01-013 and WPVS 007 are roughly consistent with the main sequence, while ESO 399-IG20, MS 22549-3712, and TON S180 show lower specific SFRs, intermediate to the main sequence and the red quiescent galaxies. The host galaxy metallicities, derived for the two sources with sufficient data quality (ESO 399-IG20 and MCG-05-01-013), indicate central oxygen abundances just below the low-redshift mass-metallicity relation. Based on this initial case study, we outline a comparison of AGN and host galaxy parameters as a starting point for future extended NLS1 studies with similar methods.

Structure-guided wavelength tuning in far-red fluorescent proteins

PubMed Central

Ng, Ho-Leung; Lin, Michael Z.

2017-01-01

In recent years, protein engineers have succeeded in tuning the excitation spectra of natural fluorescent proteins from green wavelengths into orange and red wavelengths, resulting in the creation of a series of fluorescent proteins with emission in the far-red portions of the optical spectrum. These results have arisen from the synergistic combination of structural knowledge of fluorescent proteins, chemical intuition, and high-throughput screening methods. Here we review structural features found in autocatalytic far-red fluorescent proteins, and discuss how they add to our understanding of the biophysical mechanisms of wavelength tuning in biological chromophores. PMID:27468111

The importance of satellite quenching for the build-up of the red sequence of present-day galaxies

NASA Astrophysics Data System (ADS)

van den Bosch, Frank C.; Aquino, Daniel; Yang, Xiaohu; Mo, H. J.; Pasquali, Anna; McIntosh, Daniel H.; Weinmann, Simone M.; Kang, Xi

2008-06-01

According to the current paradigm, galaxies initially form as disc galaxies at the centres of their own dark matter haloes. During their subsequent evolution, they may undergo a transformation to a red, early-type galaxy, thus giving rise to the build-up of the red sequence. Two important, outstanding questions are (i) which transformation mechanisms are most important and (ii) in what environment do they occur. In this paper, we study the impact of transformation mechanisms that operate only on satellite galaxies, such as strangulation, ram-pressure stripping and galaxy harassment. Using a large galaxy group catalogue constructed from the Sloan Digital Sky Survey, we compare the colours and concentrations of satellites galaxies to those of central galaxies of the same stellar mass, adopting the hypothesis that the latter are the progenitors of the former. On average, satellite galaxies are redder and more concentrated than central galaxies of the same stellar mass, indicating that satellite-specific transformation processes do indeed operate. Central-satellite pairs that are matched in both stellar mass and colour, however, show no average concentration difference, indicating that the transformation mechanisms operating on satellites affect colour more than morphology. We also find that the colour and concentration differences of matched central-satellite pairs are completely independent of the mass of the host halo (not to be confused with the subhalo) of the satellite galaxy, indicating that satellite-specific transformation mechanisms are equally efficient in host haloes of all masses. This strongly rules against mechanisms that are thought to operate only in very massive haloes, such as ram-pressure stripping or harassment. Instead, we argue that strangulation is the main transformation mechanism for satellite galaxies. Finally, we determine the relative importance of satellite quenching for the build-up of the red sequence. We find that roughly 70 per cent of red-sequence satellite galaxies with M* ~ 109h-2Msolar had their star formation quenched as satellites. This drops rapidly with increasing stellar mass, reaching virtually zero at M* ~ 1011h-2Msolar. Therefore, a very significant fraction of red satellite galaxies were already quenched before they became a satellite.

Simultaneous determination of hemolysis and hematocrit in extracorporeal circulation by plasma surface reflectance spectroscopy.

PubMed

Sakota, Daisuke; Kani, Yuki; Kosaka, Ryo; Nishida, Masahiro; Maruyama, Osamu

2013-01-01

To achieve quantitative non-invasive optical diagnosis of blood abnormalities during extracorporeal circulation therapies, plasma surface reflectance spectroscopy was developed by implementing oblique-incidence optical fiber reflectometry on the surface of circulating blood. The reflected light in the wavelength range from 450 to 600 nm changed with respect to the plasma free hemoglobin level and could be used to quantify the free hemoglobin at an accuracy of 5.7 ± 3.5 mg/dL. In contrast, the spectrum did not changed by varying the hematocrit. In the wavelength range from 600 to 800 nm, the obtained spectrum was affected by both the hematocrit change and hemolysis. The linear correlation between the hematocrit value and the spectrum was confirmed at R(2) = 0.99. The feasibility of determining of the hematocrit of arbitrary hemolyzed blood was confirmed. The developed system permits the extraction of the optical characteristics of both plasma and red blood cells without centrifugation. The study establishes non-invasive optical diagnostics capable of analyzing the optical properties of both plasma and red blood cells.

Lacquer polishing of X-ray optics

NASA Technical Reports Server (NTRS)

Catura, R. C.; Joki, E. G.; Roethig, D. T.; Brookover, W. J.

1987-01-01

Techniques for polishing figured X-ray optics by a lacquer-coating process are described. This acrylic lacquer coating has been applied with an optical quality of an eighth-wave in red light and very effectively covers surface roughness with spatial wavelengths less than about 0.2 mm. Tungsten films have been deposited on the lacquer coatings to provide highly efficient X-ray reflectivity.

FIRST RESULTS FROM Z -FOURGE : DISCOVERY OF A CANDIDATE CLUSTER AT z = 2.2 IN COSMOS

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

Spitler, Lee R.; Glazebrook, Karl; Poole, Gregory B.

2012-04-01

We report the first results from the Z -FOURGE survey: the discovery of a candidate galaxy cluster at z = 2.2 consisting of two compact overdensities with red galaxies detected at {approx}> 20{sigma} above the mean surface density. The discovery was made possible by a new deep (K{sub s} {approx}< 24.8 AB 5{sigma}) Magellan/FOURSTAR near-IR imaging survey with five custom medium-bandwidth filters. The filters pinpoint the location of the Balmer/4000 A break in evolved stellar populations at 1.5 < z < 3.5, yielding significantly more accurate photometric redshifts than possible with broadband imaging alone. The overdensities are within 1' ofmore » each other in the COSMOS field and appear to be embedded in a larger structure that contains at least one additional overdensity ({approx}10{sigma}). Considering the global properties of the overdensities, the z = 2.2 system appears to be the most distant example of a galaxy cluster with a population of red galaxies. A comparison to a large {Lambda}CDM simulation suggests that the system may consist of merging subclusters, with properties in between those of z > 2 protoclusters with more diffuse distributions of blue galaxies and the lower-redshift galaxy clusters with prominent red sequences. The structure is completely absent in public optical catalogs in COSMOS and only weakly visible in a shallower near-IR survey. The discovery showcases the potential of deep near-IR surveys with medium-band filters to advance the understanding of environment and galaxy evolution at z > 1.5.« less

Measurements of spectral responses for developing fiber-optic pH sensor

NASA Astrophysics Data System (ADS)

Yoo, Wook Jae; Heo, Ji Yeon; Jang, Kyoung Won; Seo, Jeong Ki; Moon, Jin Soo; Park, Jang-Yeon; Park, Byung Gi; Cho, Seunghyun; Lee, Bongsoo

2011-01-01

In this study, we have fabricated a fiber-optic pH sensor, which is composed of a light source, a pH-sensing probe, plastic optical fibers and a spectrometer, for determining the degree of infection by Helicobacter pylori in the stomach. As pH indicators, phenol red and m-cresol purple are used, and pH liquid solutions are prepared by mixing phenol red or m-cresol purple solutions and various kinds of pH buffer solutions. The light emitted by a light source is guided by plastic optical fibers to the pH liquid solution, and the optical characteristic of a reflected light is changed according to the color variations of the pH indicator in the pH-sensing probe. Therefore, we have measured the intensities and wavelength shifts of the reflected lights, which change according to the color variations of indicators at different pH values, by using a spectrometer for spectral analysis. Also, the relationships between the pH values of liquid solutions and the optical properties of the modulated lights are obtained on the basis of the changes of the colors of indicators.

Automatic real time evaluation of red blood cell elasticity by optical tweezers

NASA Astrophysics Data System (ADS)

Moura, Diógenes S.; Silva, Diego C. N.; Williams, Ajoke J.; Bezerra, Marcos A. C.; Fontes, Adriana; de Araujo, Renato E.

2015-05-01

Optical tweezers have been used to trap, manipulate, and measure individual cell properties. In this work, we show that the association of a computer controlled optical tweezers system with image processing techniques allows rapid and reproducible evaluation of cell deformability. In particular, the deformability of red blood cells (RBCs) plays a key role in the transport of oxygen through the blood microcirculation. The automatic measurement processes consisted of three steps: acquisition, segmentation of images, and measurement of the elasticity of the cells. An optical tweezers system was setup on an upright microscope equipped with a CCD camera and a motorized XYZ stage, computer controlled by a Labview platform. On the optical tweezers setup, the deformation of the captured RBC was obtained by moving the motorized stage. The automatic real-time homemade system was evaluated by measuring RBCs elasticity from normal donors and patients with sickle cell anemia. Approximately 150 erythrocytes were examined, and the elasticity values obtained by using the developed system were compared to the values measured by two experts. With the automatic system, there was a significant time reduction (60 × ) of the erythrocytes elasticity evaluation. Automated system can help to expand the applications of optical tweezers in hematology and hemotherapy.

The distant red galaxy neighbour population of 1 <~ z <~ 2 QSOs and optically obscured sources

NASA Astrophysics Data System (ADS)

Bornancini, Carlos G.; García Lambas, Diego

2007-05-01

We study the distant red galaxy (DRG; J - Ks > 2.3) neighbour population of quasi-stellar objects (QSOs) selected from the Sloan Digital Sky Survey (SDSS) in the redshift range 1 <~ z <~ 2. We perform a similar analysis for optically obscured active galactic nuclei (AGNs; i.e. with a limiting magnitude I > 24) detected in the mid-infrared (24 μm) with the Spitzer Space Telescope and a mean redshift z ~ 2.2 in the Flamingos Extragalactic Survey (FLAMEX). Both QSOs and obscured AGN target samples cover 4.7 deg2 in the same region of the sky. We find a significant difference in the environment of these two target samples. Neighbouring galaxies close to QSOs tend to be bluer than galaxies in optically obscured source environments. We also present results on the cross-correlation function of DRGs around QSOs and optically faint mid-infrared sources. The corresponding correlation length obtained for the QSO sample targets is r0 = 5.4 +/- 1.6 Mpc h-1 and a slope of γ = 1.94 +/- 0.10. For the optically obscured galaxy sample, we find r0 = 8.9 +/- 1.4 Mpc h-1 and a slope of γ = 2.27 +/- 0.20. These results indicate that optically faint obscured sources are located in denser environment of evolved red galaxies compared to QSOs. Based on observations and/or data products by the Flamingos Extragalactic Survey. FLAMINGOS was designed and constructed by the IR instrumentation group (PI: R. Elston) at the University of Florida, Department of Astronomy, with support from NSF grant AST97-31180 and Kitt Peak National Observatory. E-mail: bornancini@oac.uncor.edu

An optical water type framework for selecting and blending retrievals from bio-optical algorithms in lakes and coastal waters.

PubMed

Moore, Timothy S; Dowell, Mark D; Bradt, Shane; Verdu, Antonio Ruiz

2014-03-05

Bio-optical models are based on relationships between the spectral remote sensing reflectance and optical properties of in-water constituents. The wavelength range where this information can be exploited changes depending on the water characteristics. In low chlorophyll- a waters, the blue/green region of the spectrum is more sensitive to changes in chlorophyll- a concentration, whereas the red/NIR region becomes more important in turbid and/or eutrophic waters. In this work we present an approach to manage the shift from blue/green ratios to red/NIR-based chlorophyll- a algorithms for optically complex waters. Based on a combined in situ data set of coastal and inland waters, measures of overall algorithm uncertainty were roughly equal for two chlorophyll- a algorithms-the standard NASA OC4 algorithm based on blue/green bands and a MERIS 3-band algorithm based on red/NIR bands-with RMS error of 0.416 and 0.437 for each in log chlorophyll- a units, respectively. However, it is clear that each algorithm performs better at different chlorophyll- a ranges. When a blending approach is used based on an optical water type classification, the overall RMS error was reduced to 0.320. Bias and relative error were also reduced when evaluating the blended chlorophyll- a product compared to either of the single algorithm products. As a demonstration for ocean color applications, the algorithm blending approach was applied to MERIS imagery over Lake Erie. We also examined the use of this approach in several coastal marine environments, and examined the long-term frequency of the OWTs to MODIS-Aqua imagery over Lake Erie.

An optical water type framework for selecting and blending retrievals from bio-optical algorithms in lakes and coastal waters

PubMed Central

Moore, Timothy S.; Dowell, Mark D.; Bradt, Shane; Verdu, Antonio Ruiz

2014-01-01

Bio-optical models are based on relationships between the spectral remote sensing reflectance and optical properties of in-water constituents. The wavelength range where this information can be exploited changes depending on the water characteristics. In low chlorophyll-a waters, the blue/green region of the spectrum is more sensitive to changes in chlorophyll-a concentration, whereas the red/NIR region becomes more important in turbid and/or eutrophic waters. In this work we present an approach to manage the shift from blue/green ratios to red/NIR-based chlorophyll-a algorithms for optically complex waters. Based on a combined in situ data set of coastal and inland waters, measures of overall algorithm uncertainty were roughly equal for two chlorophyll-a algorithms—the standard NASA OC4 algorithm based on blue/green bands and a MERIS 3-band algorithm based on red/NIR bands—with RMS error of 0.416 and 0.437 for each in log chlorophyll-a units, respectively. However, it is clear that each algorithm performs better at different chlorophyll-a ranges. When a blending approach is used based on an optical water type classification, the overall RMS error was reduced to 0.320. Bias and relative error were also reduced when evaluating the blended chlorophyll-a product compared to either of the single algorithm products. As a demonstration for ocean color applications, the algorithm blending approach was applied to MERIS imagery over Lake Erie. We also examined the use of this approach in several coastal marine environments, and examined the long-term frequency of the OWTs to MODIS-Aqua imagery over Lake Erie. PMID:24839311

Experimental demonstration of tunable multiple optical orthogonal codes sequences-based optical label for optical packets switching

NASA Astrophysics Data System (ADS)

Zhang, Chongfu; Qiu, Kun; Zhou, Heng; Ling, Yun; Wang, Yawei; Xu, Bo

2010-03-01

In this paper, the tunable multiple optical orthogonal codes sequences (MOOCS)-based optical label for optical packet switching (OPS) (MOOCS-OPS) is experimentally demonstrated for the first time. The tunable MOOCS-based optical label is performed by using fiber Bragg grating (FBG)-based optical en/decoders group and optical switches configured by using Field Programmable Gate Array (FPGA), and the optical label is erased by using Semiconductor Optical Amplifier (SOA). Some waveforms of the MOOCS-based optical label, optical packet including the MOOCS-based optical label and the payloads are obtained, the switching control mechanism and the switching matrix are discussed, the bit error rate (BER) performance of this system is also studied. These experimental results show that the tunable MOOCS-OPS scheme is effective.

Realization of 95% of the Rec. 2020 color gamut in a highly efficient LCD using a patterned quantum dot film.

PubMed

Kim, Hyo-Jun; Shin, Min-Ho; Lee, Jae-Yong; Kim, Ji-Hoon; Kim, Young-Joo

2017-05-15

An optically efficient liquid-crystal display (LCD) structure using a patterned quantum dot (QD) film and a short-pass filter (SPF) was proposed and fabricated. The patterned QD film contributed to the generation of 95% in the area ratio (or 90% in the coverage ratio) of the Rec. 2020 color gamut. This was achieved by avoiding the problem of interaction between white backlight and broad transmittance spectra of color filters (CFs) as seen in a conventional LCD with a mixed QD film as a reference. The patterned QD film can maintain the narrow bandwidth of the green and the red QD colors before passing through the CFs. Additionally, the optical intensities of the red, green, and blue spectra were enhanced to 1.63, 1.72, and 2.16 times the reference LCD values, respectively. This was a result of separated emission of the red and green patterned QD film and reflection of the red and green light to the forward direction by the SPF.

Novel phytochrome sequences in Arabidopsis thaliana: Structure, evolution, and differential expression of a plant regulatory photoreceptor family

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

Sharrock, R.A.; Quail, P.H.

1989-01-01

Phytochrome is a plant regulatory photoreceptor that mediates red light effects on a wide variety of physiological and molecular responses. DNA blot analysis indicates that the Arabidopsis thaliana genome contains four to five phytochrome-related gene sequences. The authors have isolated and sequenced cDNA clones corresponding to three of these genes and have deduced the amino acid sequence of the full-length polypeptide encoded in each case. One of these proteins (phyA) shows 65-80% amino acid sequence identity with the major, etiolated-tissue phytochrome apoproteins described previously in other plant species. The other two polypeptides (phyB and phyC) are unique in that theymore » have low sequence identity with each other, with phyA, and with all previously described phytochromes. The phyA, phyB, and phyC proteins are of similar molecular mass, have related hydropathic profiles, and contain a conserved chromophore attachment region. However, the sequence comparison data indicate that the three phy genes diverged early in plant evolution, well before the divergence of the two major groups of angiosperms, the monocots and dicots. The steady-state level of the phyA transcript is high in dark-grown A. thaliana seedlings and is down-regulated by light. In contrast, the phyB and phyC transcripts are present at lower levels and are not strongly light-regulated. These findings indicate that the red/far red light-responsive phytochrome photoreceptor system in A. thaliana, and perhaps in all higher plants, consists of a family of chromoproteins that are heterogeneous in structure and regulation.« less

RNA-seq analysis of Rubus idaeus cv. Nova: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.

PubMed

Hyun, Tae Kyung; Lee, Sarah; Kumar, Dhinesh; Rim, Yeonggil; Kumar, Ritesh; Lee, Sang Yeol; Lee, Choong Hwan; Kim, Jae-Yean

2014-10-01

Using Illumina sequencing technology, we have generated the large-scale transcriptome sequencing data containing abundant information on genes involved in the metabolic pathways in R. idaeus cv. Nova fruits. Rubus idaeus (Red raspberry) is one of the important economical crops that possess numerous nutrients, micronutrients and phytochemicals with essential health benefits to human. The molecular mechanism underlying the ripening process and phytochemical biosynthesis in red raspberry is attributed to the changes in gene expression, but very limited transcriptomic and genomic information in public databases is available. To address this issue, we generated more than 51 million sequencing reads from R. idaeus cv. Nova fruit using Illumina RNA-Seq technology. After de novo assembly, we obtained 42,604 unigenes with an average length of 812 bp. At the protein level, Nova fruit transcriptome showed 77 and 68 % sequence similarities with Rubus coreanus and Fragaria versa, respectively, indicating the evolutionary relationship between them. In addition, 69 % of assembled unigenes were annotated using public databases including NCBI non-redundant, Cluster of Orthologous Groups and Gene ontology database, suggesting that our transcriptome dataset provides a valuable resource for investigating metabolic processes in red raspberry. To analyze the relationship between several novel transcripts and the amounts of metabolites such as γ-aminobutyric acid and anthocyanins, real-time PCR and target metabolite analysis were performed on two different ripening stages of Nova. This is the first attempt using Illumina sequencing platform for RNA sequencing and de novo assembly of Nova fruit without reference genome. Our data provide the most comprehensive transcriptome resource available for Rubus fruits, and will be useful for understanding the ripening process and for breeding R. idaeus cultivars with improved fruit quality.

Photometry, Astrometry, and Discoveries of Ultracool Dwarfs in the Pan-STARRS 3π Survey

NASA Astrophysics Data System (ADS)

Best, William M. J.; Magnier, Eugene A.; Liu, Michael C.; Deacon, Niall; Aller, Kimberly; Zhang, Zhoujian; Pan-STARRS1 Builders

2018-01-01

The Pan-STARRS1 3π Survey (PS1)'s far-red optical sensitivity makes it an exceptional new resource for discovering and characterizing ultracool dwarfs. We present a PS1-based catalog of photometry and proper motions of nearly 10,000 M, L, and T dwarfs, along with our analysis of the kinematics of nearby M6-T9 dwarfs, building a comprehensive picture of the local ultracool population. We highlight some especially interesting ultracool discoveries made with PS1, including brown dwarfs with spectral types in the enigmatic L/T transition, wide companions to main sequence stars that serve as age and metallicity bechmarks for substellar models, and free-floating members of the nearby young moving groups and star-forming regions with masses down to ≈5 MJup. With its public release, PS1 will continue to be a vital tool for studying the ultracool population.

Amdoparvovirus Infection in Red Pandas ( Ailurus fulgens).

PubMed

Alex, Charles E; Kubiski, Steven V; Li, Linlin; Sadeghi, Mohammadreza; Wack, Raymund F; McCarthy, Megan A; Pesavento, Joseph B; Delwart, Eric; Pesavento, Patricia A

2018-01-01

Aleutian mink disease virus is the type species in the genus Amdoparvovirus, and in mink and other Mustelidae can cause either subclinical disease or fatal chronic immune stimulation and immune complex disease. The authors describe a novel amdoparvovirus in the endangered red panda ( Ailurus fulgens), discovered using viral metagenomics. The authors analyzed the prevalence, tissue distribution, and disease association by PCR, in situ hybridization, electron microscopy, and histology in a group of 6 red pandas from a single zoological collection. The study incorporates a fecal shedding survey and analysis of tissues from 4 necropsied animals over a 12-year span. The tentatively named red panda amdoparvovirus (RpAPV) was detected in the feces and/or tissues of all animals tested. At necropsy of 1 geriatric animal, infection was associated with pyogranulomatous peritonitis, pancreatitis, and myocarditis. Other animals had detectable low-level viral nucleic acid in lymph nodes and both oral and intestinal epithelium at the time of necropsy. Full-length genome sequences of RpAPV strains from 2 animals had 12% sequence divergence, demonstrating genetic diversity even among in-contact animals. RpAPV is a persistent infection in this cohort of red pandas, and has variable clinical expression.

Molecular Survey of Hepatozoon canis in Red Foxes (Vulpes vulpes) from Romania.

PubMed

Imre, Mirela; Dudu, Andreea; Ilie, Marius S; Morariu, Sorin; Imre, Kálmán; Dărăbuş, Gheorghe

2015-08-01

Blood samples of 119 red foxes, originating from 44 hunting grounds of 3 western counties (Arad, Hunedoara, and Timiş) of Romania, have been examined for the presence of Hepatozoon canis infection using the conventional polymerase chain reaction (PCR) of the fragment of 18S rRNA gene. Overall, 15 (12.6%) samples were found to be PCR-positive. Of the sampled hunting grounds, 29.5% (13/44) were found positive. Positive samples were recorded in all screened counties with the prevalence of 14.8% (9/61) in Arad, 9.8% (5/51) in Timiş, and 14.3% (1/7) in Hunedoara, respectively. No correlation was found (P > 0.05) between H. canis positivity and gender or territorial distribution of the infection. To confirm PCR results, 9 randomly selected amplicons were sequenced. The obtained sequences were identical to each other, confirmed the results of the conventional PCR, and showed 98-100% homology to other H. canis sequences. The results of the current survey support the role of red foxes as sylvatic reservoirs of H. canis in Romania.

Radio Emission from Red-Giant Hot Jupiters

NASA Technical Reports Server (NTRS)

Fujii, Yuka; Spiegel, David S.; Mroczkowski, Tony; Nordhaus, Jason; Zimmerman, Neil T.; Parsons, Aaron R.; Mirbabayi, Mehrdad; Madhusudhan, Nikku

2016-01-01

When planet-hosting stars evolve off the main sequence and go through the red-giant branch, the stars become orders of magnitudes more luminous and, at the same time, lose mass at much higher rates than their main sequence counterparts. Accordingly, if planetary companions exist around these stars at orbital distances of a few au, they will be heated up to the level of canonical hot Jupiters and also be subjected to a dense stellar wind. Given that magnetized planets interacting with stellar winds emit radio waves, such "Red-Giant Hot Jupiters" (RGHJs) may also be candidate radio emitters. We estimate the spectral auroral radio intensity of RGHJs based on the empirical relation with the stellar wind as well as a proposed scaling for planetary magnetic fields. RGHJs might be intrinsically as bright as or brighter than canonical hot Jupiters and about 100 times brighter than equivalent objects around main-sequence stars. We examine the capabilities of low-frequency radio observatories to detect this emission and find that the signal from an RGHJ may be detectable at distances up to a few hundred parsecs with the Square Kilometer Array.

Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea.

PubMed

Al-Rshaidat, Mamoon M D; Snider, Allison; Rosebraugh, Sydney; Devine, Amanda M; Devine, Thomas D; Plaisance, Laetitia; Knowlton, Nancy; Leray, Matthieu

2016-09-01

High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months. DNA barcoding of non-sessile specimens >2 mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2 mm - 500 μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales.

Optical thermal sensor based on cholesteric film refilled with mixture of toluene and ethanol.

PubMed

Li, Yong; Liu, Yanjun; Luo, Dan

2017-10-16

We demonstrate an optical thermal sensor based on cholesteric film refilled with mixture of toluene and ethanol. The thermal response mechanism is mainly based on the thermal expansion effect induce by toluene, where the ethanol is used for refractive index adjustment to determine the initial refection band position of cholesteric film. The ethanol-toluene mixture was used to adjust the color tunability with the temperature in relation with the habits of people (blue as cold, green as safe and red as hot). A broad temperature range of 86 °C and highly sensitivity of 1.79 nm/ °C are achieved in proposed thermal sensor, where the reflective color red-shifts from blue to red when environmental temperature increases from -6 °C to 80 °C. This battery-free thermal sensor possesses features including simple fabrication, low-cost, and broad temperature sensing range, showing potential application in scientific research and industry.

Optical properties of anthocyanin dyes on TiO2 as photosensitizers for application of dye-sensitized solar cell (DSSC)

NASA Astrophysics Data System (ADS)

Ahliha, A. H.; Nurosyid, F.; Supriyanto, A.; Kusumaningsih, T.

2018-03-01

Dye-sensitized solar cell (DSSC) is one of the alternative energy that can convert light energy into electrical energy. The component of DSSC consists of FTO substrates, TiO2, electrolyte, dye sensitizer, and counter electrode. This study aim was to determine the effect of optical properties of anthocyanin dyes on efficiency of DSSC. The dye sensitizer used can be extracted from anthocyanin pigments such as dragon fruit, black rice, and red cabbage. The red cabbage sensitizer shows lower absorbance value in the visible range (450-580 nm), than dragon fruit and black rice. The chemical structure of each dye molecules has an R group (carbonyl and hydroxyl) that forms a bond with the oxide layer. Red cabbage dye cell has the highest efficiency, 0.06% then dragon fruit and black rice, 0.02% and 0.03%.

Combining Optical Reporter Proteins with Different Half-lives to Detect Temporal Evolution of Hypoxia and Reoxygenation in Tumors

PubMed Central

Danhier, Pierre; Krishnamachary, Balaji; Bharti, Santosh; Kakkad, Samata; Mironchik, Yelena; Bhujwalla, Zaver M.

2015-01-01

Here we have developed a hypoxia response element driven imaging strategy that combined the hypoxia-driven expression of two optical reporters with different half-lives to detect temporal changes in hypoxia and hypoxia inducible factor (HIF) activity. For this purpose, human prostate cancer PC3 cells were transfected with the luciferase gene fused with an oxygen-dependent degradation domain (ODD-luc) and a variant of the enhanced green fluorescent protein (EGFP). Both ODD-luciferase and EGFP were under the promotion of a poly-hypoxia-response element sequence (5xHRE). The cells constitutively expressed tdTomato red fluorescent protein. For validating the imaging strategy, cells were incubated under hypoxia (1% O2) for 48 hours and then reoxygenated. The luciferase activity of PC3-HRE-EGFP/HRE-ODD-luc/tdtomato cells detected by bioluminescent imaging rapidly decreased after reoxygenation, whereas EGFP levels in these cells remained stable for several hours. After in vitro validation, PC3-HRE-EGFP/HRE-ODD-luc/tdtomato tumors were implanted subcutaneously and orthotopically in nude male mice and imaged in vivo and ex vivo using optical imaging in proof-of-principle studies to demonstrate differences in optical patterns between EGFP expression and bioluminescence. This novel "timer" imaging strategy of combining the short-lived ODD-luciferase and the long-lived EGFP can provide a time frame of HRE activation in PC3 prostate cancer cells and will be useful to understand the temporal changes in hypoxia and HIF activity during cancer progression and following treatments including HIF targeting strategies. PMID:26696369

Cloning and sequence analysis demonstrate the chromate reduction ability of a novel chromate reductase gene from Serratia sp.

PubMed

Deng, Peng; Tan, Xiaoqing; Wu, Ying; Bai, Qunhua; Jia, Yan; Xiao, Hong

2015-03-01

The ChrT gene encodes a chromate reductase enzyme which catalyzes the reduction of Cr(VI). The chromate reductase is also known as flavin mononucleotide (FMN) reductase (FMN_red). The aim of the present study was to clone the full-length ChrT DNA from Serratia sp. CQMUS2 and analyze the deduced amino acid sequence and three-dimensional structure. The putative ChrT gene fragment of Serratia sp. CQMUS2 was isolated by polymerase chain reaction (PCR), according to the known FMN_red gene sequence from Serratia sp. AS13. The flanking sequences of the ChrT gene were obtained by high efficiency TAIL-PCR, while the full-length gene of ChrT was cloned in Escherichia coli for subsequent sequencing. The nucleotide sequence of ChrT was submitted onto GenBank under the accession number, KF211434. Sequence analysis of the gene and amino acids was conducted using the Basic Local Alignment Search Tool, and open reading frame (ORF) analysis was performed using ORF Finder software. The ChrT gene was found to be an ORF of 567 bp that encodes a 188-amino acid enzyme with a calculated molecular weight of 20.4 kDa. In addition, the ChrT protein was hypothesized to be an NADPH-dependent FMN_red and a member of the flavodoxin-2 superfamily. The amino acid sequence of ChrT showed high sequence similarity to the FMN reductase genes of Klebsiella pneumonia and Raoultella ornithinolytica , which belong to the flavodoxin-2 superfamily. Furthermore, ChrT was shown to have a 85.6% similarity to the three-dimensional structure of Escherichia coli ChrR, sharing four common enzyme active sites for chromate reduction. Therefore, ChrT gene cloning and protein structure determination demonstrated the ability of the gene for chromate reduction. The results of the present study provide a basis for further studies on ChrT gene expression and protein function.

Cloning and sequence analysis demonstrate the chromate reduction ability of a novel chromate reductase gene from Serratia sp

PubMed Central

DENG, PENG; TAN, XIAOQING; WU, YING; BAI, QUNHUA; JIA, YAN; XIAO, HONG

2015-01-01

The ChrT gene encodes a chromate reductase enzyme which catalyzes the reduction of Cr(VI). The chromate reductase is also known as flavin mononucleotide (FMN) reductase (FMN_red). The aim of the present study was to clone the full-length ChrT DNA from Serratia sp. CQMUS2 and analyze the deduced amino acid sequence and three-dimensional structure. The putative ChrT gene fragment of Serratia sp. CQMUS2 was isolated by polymerase chain reaction (PCR), according to the known FMN_red gene sequence from Serratia sp. AS13. The flanking sequences of the ChrT gene were obtained by high efficiency TAIL-PCR, while the full-length gene of ChrT was cloned in Escherichia coli for subsequent sequencing. The nucleotide sequence of ChrT was submitted onto GenBank under the accession number, KF211434. Sequence analysis of the gene and amino acids was conducted using the Basic Local Alignment Search Tool, and open reading frame (ORF) analysis was performed using ORF Finder software. The ChrT gene was found to be an ORF of 567 bp that encodes a 188-amino acid enzyme with a calculated molecular weight of 20.4 kDa. In addition, the ChrT protein was hypothesized to be an NADPH-dependent FMN_red and a member of the flavodoxin-2 superfamily. The amino acid sequence of ChrT showed high sequence similarity to the FMN reductase genes of Klebsiella pneumonia and Raoultella ornithinolytica, which belong to the flavodoxin-2 superfamily. Furthermore, ChrT was shown to have a 85.6% similarity to the three-dimensional structure of Escherichia coli ChrR, sharing four common enzyme active sites for chromate reduction. Therefore, ChrT gene cloning and protein structure determination demonstrated the ability of the gene for chromate reduction. The results of the present study provide a basis for further studies on ChrT gene expression and protein function. PMID:25667630

Study on the characteristic and application of DFB semiconductor lasers under optical injection for microwave photonics

NASA Astrophysics Data System (ADS)

Pu, Tao; Wang, Wei wei

2018-01-01

In order to apply optical injection effect in Microwave Photonics system, The red-shift effect of the cavity mode of the DFB semiconductor laser under single-frequency optical injection is studied experimentally, and the red-shift curve of the cavity mode is measured. The wavelength-selective amplification property of the DFB semiconductor laser under multi-frequency optical injection is also investigated, and the gain curves for the injected signals in different injection ratios are measured in the experiment. A novel and simple structure to implement a single-passband MPF with wideband tunability based on the wavelength-selective amplification of a DFB semiconductor laser under optical injection is proposed and experimentally demonstrated. MPFs with center frequency tuned from 13 to 41 GHz are realized in the experiment. A wideband and frequency-tunable optoelectronic oscillator based on a directly modulated distributed feedback (DFB) semiconductor laser under optical injection is proposed and experimentally demonstrated. By optical injection, the relaxation oscillation frequency of the DFB laser is enhanced and its high modulation efficiency makes the loop oscillate without the necessary of the electrical filter. An experiment is performed; microwave signals with frequency tuned from 5.98 to 15.22 GHz are generated by adjusting the injection ratio and frequency detuning between the master and slave lasers.

Optical waveguide and room temperature high-quality nanolasers from tin-catalyzed CdSSe nanostructures

NASA Astrophysics Data System (ADS)

Guo, Pengfei; Shen, Xia; Zhang, Baolong; Sun, Haibin; Zou, Zhijun; Yang, Wenchao; Gong, Ke; Luo, Yongsong

2018-05-01

A simple two-step CVD method is developed to realize the growth of high-quality tin-catalyzed CdSSe alloy nanowires. Microstructural characterizations demonstrate that these wires are high-quality crystalline nanostructures. Local photoluminescence investigation of these nanostructures shows a typical band edge emission at 656 nm with a full-width at half-maximum of 22.3 nm. Optical waveguide measurement along an individual nanowire indicates that the output signal of the guided light has a rapid linear decrease accompanied with maximum red-shift about 109 meV after the transmission of 102 μm. This obvious red-shift is caused by the intensive band-tail absorption during the optical transmission process. Moreover, optically pumped nanolasers are successfully realized at room temperature based on these unique wires, further demonstrating the achievement of stimulated emission from spontaneous emission, promoted by the pump power intensity. This work may find a simple route to the manufacture of superior nanowires for applications in waveguide and integrated photonic devices.

High efficient OLED displays prepared with the air-gapped bridges on quantum dot patterns for optical recycling

PubMed Central

Kim, Hyo-Jun; Shin, Min-Ho; Kim, Joo-Suc; Kim, Se-Eun; Kim, Young-Joo

2017-01-01

An optically efficient structure was proposed and fabricated to realize high brightness organic light emitting diode (OLED) displays based on a white OLED prepared with the air-gapped bridges on the quantum dot (QD) patterns. Compared with a conventional white OLED display, in our experiments, the optical intensity of the proposed OLED display shows the enhancement of 58.2% in the red color and 16.8% in the green color after applying the air-gapped bridge structure on QD patterns of 20 wt% concentration. This enhancement comes from the two facts that the QD patterns downconvert unnecessary blue or blue/green light to the required green or red light and the air-gapped bridges increase the color conversion efficiency of QDs by optical recycling using total internal reflection (TIR) at the interface. In addition, the color gamut of the proposed OLED display increases from 65.5 to 75.9% (NTSC x, y ratio) due to the narrow emission spectra of QDs. PMID:28211516

Optical waveguide and room temperature high-quality nanolasers from tin-catalyzed CdSSe nanostructures.

PubMed

Guo, Pengfei; Shen, Xia; Zhang, Baolong; Sun, Haibin; Zou, Zhijun; Yang, Wenchao; Gong, Ke; Luo, Yongsong

2018-05-04

A simple two-step CVD method is developed to realize the growth of high-quality tin-catalyzed CdSSe alloy nanowires. Microstructural characterizations demonstrate that these wires are high-quality crystalline nanostructures. Local photoluminescence investigation of these nanostructures shows a typical band edge emission at 656 nm with a full-width at half-maximum of 22.3 nm. Optical waveguide measurement along an individual nanowire indicates that the output signal of the guided light has a rapid linear decrease accompanied with maximum red-shift about 109 meV after the transmission of 102 μm. This obvious red-shift is caused by the intensive band-tail absorption during the optical transmission process. Moreover, optically pumped nanolasers are successfully realized at room temperature based on these unique wires, further demonstrating the achievement of stimulated emission from spontaneous emission, promoted by the pump power intensity. This work may find a simple route to the manufacture of superior nanowires for applications in waveguide and integrated photonic devices.

High efficient OLED displays prepared with the air-gapped bridges on quantum dot patterns for optical recycling

NASA Astrophysics Data System (ADS)

Kim, Hyo-Jun; Shin, Min-Ho; Kim, Joo-Suc; Kim, Se-Eun; Kim, Young-Joo

2017-02-01

An optically efficient structure was proposed and fabricated to realize high brightness organic light emitting diode (OLED) displays based on a white OLED prepared with the air-gapped bridges on the quantum dot (QD) patterns. Compared with a conventional white OLED display, in our experiments, the optical intensity of the proposed OLED display shows the enhancement of 58.2% in the red color and 16.8% in the green color after applying the air-gapped bridge structure on QD patterns of 20 wt% concentration. This enhancement comes from the two facts that the QD patterns downconvert unnecessary blue or blue/green light to the required green or red light and the air-gapped bridges increase the color conversion efficiency of QDs by optical recycling using total internal reflection (TIR) at the interface. In addition, the color gamut of the proposed OLED display increases from 65.5 to 75.9% (NTSC x, y ratio) due to the narrow emission spectra of QDs.

High efficient OLED displays prepared with the air-gapped bridges on quantum dot patterns for optical recycling.

PubMed

Kim, Hyo-Jun; Shin, Min-Ho; Kim, Joo-Suc; Kim, Se-Eun; Kim, Young-Joo

2017-02-17

An optically efficient structure was proposed and fabricated to realize high brightness organic light emitting diode (OLED) displays based on a white OLED prepared with the air-gapped bridges on the quantum dot (QD) patterns. Compared with a conventional white OLED display, in our experiments, the optical intensity of the proposed OLED display shows the enhancement of 58.2% in the red color and 16.8% in the green color after applying the air-gapped bridge structure on QD patterns of 20 wt% concentration. This enhancement comes from the two facts that the QD patterns downconvert unnecessary blue or blue/green light to the required green or red light and the air-gapped bridges increase the color conversion efficiency of QDs by optical recycling using total internal reflection (TIR) at the interface. In addition, the color gamut of the proposed OLED display increases from 65.5 to 75.9% (NTSC x, y ratio) due to the narrow emission spectra of QDs.

Real-time biodetection using a smartphone-based dual-color surface plasmon resonance sensor

NASA Astrophysics Data System (ADS)

Liu, Qiang; Yuan, Huizhen; Liu, Yun; Wang, Jiabin; Jing, Zhenguo; Peng, Wei

2018-04-01

We proposed a compact and cost-effective red-green dual-color fiber optic surface plasmon resonance (SPR) sensor based on the smartphone. Inherent color selectivity of phone cameras was utilized for real-time monitoring of red and green color channels simultaneously, which can reduce the chance of false detection and improve the sensitivity. Because there are no external prisms, complex optical lenses, or diffraction grating, simple optical configuration is realized. It has a linear response in a refractive index range of 1.326 to 1.351 (R2 = 0.991) with a resolution of 2.3 × 10 - 4 RIU. We apply it for immunoglobulin G (IgG) concentration measurement. Experimental results demonstrate that a linear SPR response was achieved for IgG concentrations varying from 0.02 to 0.30 mg / ml with good repeatability. It may find promising applications in the fields of public health and environment monitoring owing to its simple optics design and applicability in real-time, label-free biodetection.

Coupling quantum dots to optical fiber: Low pump threshold laser in the red with a near top hat beam profile

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

Cheng, H., E-mail: harvey6117@gmail.com; Laboratory for Optical Physics and Engineering, Department of Electrical and Computer Engineering, University of Illinois, Urbana, Illinois 61801; Mironov, A. E.

2015-02-23

Direct coupling of the optical field in a ∼244 nm thick, CdSe/ZnS quantum dot film to an optical fiber has yielded lasing in the red (λ ∼ 644 nm) with a threshold pump energy density < 2.6 mJ cm{sup −2}. Comprising 28–31 layers of ∼8 nm diameter quantum dots deposited onto the exterior surface of a 125 μm diameter coreless silica fiber, this free-running oscillator produces 134 nJ in 3.6 ns FWHM pulses which correspond to 37 W of peak power from an estimated gain volume of ∼4.5 × 10{sup −7} cm{sup 3}. Lasing was confirmed by narrowing of the output optical radiation in both the spectral and temporal domains, and the lasermore » beam intensity profile approximates a top hat.« less

Taxonomic distribution and origins of the extended LHC (light-harvesting complex) antenna protein superfamily

PubMed Central

2010-01-01

Background The extended light-harvesting complex (LHC) protein superfamily is a centerpiece of eukaryotic photosynthesis, comprising the LHC family and several families involved in photoprotection, like the LHC-like and the photosystem II subunit S (PSBS). The evolution of this complex superfamily has long remained elusive, partially due to previously missing families. Results In this study we present a meticulous search for LHC-like sequences in public genome and expressed sequence tag databases covering twelve representative photosynthetic eukaryotes from the three primary lineages of plants (Plantae): glaucophytes, red algae and green plants (Viridiplantae). By introducing a coherent classification of the different protein families based on both, hidden Markov model analyses and structural predictions, numerous new LHC-like sequences were identified and several new families were described, including the red lineage chlorophyll a/b-binding-like protein (RedCAP) family from red algae and diatoms. The test of alternative topologies of sequences of the highly conserved chlorophyll-binding core structure of LHC and PSBS proteins significantly supports the independent origins of LHC and PSBS families via two unrelated internal gene duplication events. This result was confirmed by the application of cluster likelihood mapping. Conclusions The independent evolution of LHC and PSBS families is supported by strong phylogenetic evidence. In addition, a possible origin of LHC and PSBS families from different homologous members of the stress-enhanced protein subfamily, a diverse and anciently paralogous group of two-helix proteins, seems likely. The new hypothesis for the evolution of the extended LHC protein superfamily proposed here is in agreement with the character evolution analysis that incorporates the distribution of families and subfamilies across taxonomic lineages. Intriguingly, stress-enhanced proteins, which are universally found in the genomes of green plants, red algae, glaucophytes and in diatoms with complex plastids, could represent an important and previously missing link in the evolution of the extended LHC protein superfamily. PMID:20673336

Are optical indices good proxies of seasonal changes in carbon fluxes and stress-related physiological status in a beech forest?

PubMed

Nestola, E; Scartazza, A; Di Baccio, D; Castagna, A; Ranieri, A; Cammarano, M; Mazzenga, F; Matteucci, G; Calfapietra, C

2018-01-15

This study investigates the functionality of a Mediterranean-mountain beech forest in Central Italy using simultaneous determinations of optical measurements, carbon (C) fluxes, leaf eco-physiological and biochemical traits during two growing seasons (2014-2015). Meteorological variables showed significant differences between the two growing seasons, highlighting a heat stress coupled with a reduced water availability in mid-summer 2015. As a result, a different C sink capacity of the forest was observed between the two years of study, due to the differences in stressful conditions and the related plant physiological status. Spectral indices related to vegetation (VIs, classified in structural, chlorophyll and carotenoid indices) were computed at top canopy level and used to track CO 2 fluxes and physiological changes. Optical indices related to structure (EVI 2, RDVI, DVI and MCARI 1) were found to better track Net Ecosystem Exchange (NEE) variations for 2014, while indices related to chlorophylls (SR red edge, CL red edge, MTCI and DR) provided better results for 2015. This suggests that when environmental conditions are not limiting for forest sink capacity, structural parameters are more strictly connected to C uptake, while under stress conditions indices related to functional features (e.g., chlorophyll content) become more relevant. Chlorophyll indices calculated with red edge bands (SR red edge, NDVI red edge, DR, CL red edge) resulted to be highly correlated with leaf nitrogen content (R 2 >0.70), while weaker, although significant, correlations were found with chlorophyll content. Carotenoid indices (PRI and PSRI) were strongly correlated with both chlorophylls and carotenoids content, suggesting that these indices are good proxies of the shifting pigment composition related to changes in soil moisture, heat stress and senescence. Our work suggests the importance of integrating different methods as a successful approach to understand how changing climatic conditions in the Mediterranean mountain region will impact on forest conditions and functionality. Copyright © 2017 Elsevier B.V. All rights reserved.

Do genes lie? Mitochondrial capture masks the Red Sea collector urchin's true identity (Echinodermata: Echinoidea: Tripneustes).

PubMed

Bronstein, Omri; Kroh, Andreas; Haring, Elisabeth

2016-11-01

Novel COI and bindin sequences of the Red Sea collector echinoid Tripneustes gratilla elatensis are used to show that (1) discordance between mitochondrial and nuclear loci exists in this echinoid genus, (2) Tripneustes gratilla as currently defined possibly comprises a complex of cryptic species, and (3) Red Sea Tripneustes form a genetically distinct clade in the bindin tree, which diverged from other Tripneustes clades at least 2-4million years ago. Morphological reassessment of T. gratilla elatensis shows perfect congruence between identification based on skeletal features and genetic data based on a nuclear marker sequence. Hence the Red Sea Tripneustes subspecies established by Dafni in 1983 is a distinct biological unit. All T. g. elatensis samples analyzed are highly similar to or share mtDNA haplotypes with Philippine T. g. gratilla, as do representatives from other edge-of-range occurrences. This lack of genetic structure in Indo-Pacific Tripneustes is interpreted as a result of wide-spread mitochondrial introgression. New fossil specimens from the Red Sea area confirm the sympatric occurrence of T. g. elatensis and T. g. gratilla in the northern Red Sea during Late Pleistocene, identifying a possible timing for the introgression. In addition, present-day distribution shows a contact zone in the Southern Red Sea (in the Dahlak Archipelago). T. g. elatensis, is yet another example of a Red Sea taxon historically identified as conspecific with its Indo-Pacific relatives, but which turned out to be a morphologically and genetically distinct endemic taxon, suggesting that the level of endemism in the Red Sea may still be underestimated. Copyright © 2016 Elsevier Inc. All rights reserved.

High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

NASA Astrophysics Data System (ADS)

Kim, Kyoohyun; Yoon, HyeOk; Diez-Silva, Monica; Dao, Ming; Dasari, Ramachandra R.; Park, YongKeun

2014-01-01

We present high-resolution optical tomographic images of human red blood cells (RBC) parasitized by malaria-inducing Plasmodium falciparum (Pf)-RBCs. Three-dimensional (3-D) refractive index (RI) tomograms are reconstructed by recourse to a diffraction algorithm from multiple two-dimensional holograms with various angles of illumination. These 3-D RI tomograms of Pf-RBCs show cellular and subcellular structures of host RBCs and invaded parasites in fine detail. Full asexual intraerythrocytic stages of parasite maturation (ring to trophozoite to schizont stages) are then systematically investigated using optical diffraction tomography algorithms. These analyses provide quantitative information on the structural and chemical characteristics of individual host Pf-RBCs, parasitophorous vacuole, and cytoplasm. The in situ structural evolution and chemical characteristics of subcellular hemozoin crystals are also elucidated.

Phase shifting white light interferometry using colour CCD for optical metrology and bio-imaging applications

NASA Astrophysics Data System (ADS)

Upputuri, Paul Kumar; Pramanik, Manojit

2018-02-01

Phase shifting white light interferometry (PSWLI) has been widely used for optical metrology applications because of their precision, reliability, and versatility. White light interferometry using monochrome CCD makes the measurement process slow for metrology applications. WLI integrated with Red-Green-Blue (RGB) CCD camera is finding imaging applications in the fields optical metrology and bio-imaging. Wavelength dependent refractive index profiles of biological samples were computed from colour white light interferograms. In recent years, whole-filed refractive index profiles of red blood cells (RBCs), onion skin, fish cornea, etc. were measured from RGB interferograms. In this paper, we discuss the bio-imaging applications of colour CCD based white light interferometry. The approach makes the measurement faster, easier, cost-effective, and even dynamic by using single fringe analysis methods, for industrial applications.

Evaluation of mouse red blood cell and platelet counting with an automated hematology analyzer.

PubMed

Fukuda, Teruko; Asou, Eri; Nogi, Kimiko; Goto, Kazuo

2017-10-07

An evaluation of mouse red blood cell (RBC) and platelet (PLT) counting with an automated hematology analyzer was performed with three strains of mice, C57BL/6 (B6), BALB/c (BALB) and DBA/2 (D2). There were no significant differences in RBC and PLT counts between manual and automated optical methods in any of the samples, except for D2 mice. For D2, RBC counts obtained using the manual method were significantly lower than those obtained using the automated optical method (P<0.05), and PLT counts obtained using the manual method were higher than those obtained using the automated optical method (P<0.05). An automated hematology analyzer can be used for RBC and PLT counting; however, an appropriate method should be selected when D2 mice samples are used.

ASPIRE - Airborne Spectro-Polarization InfraRed Experiment

NASA Astrophysics Data System (ADS)

DeLuca, E.; Cheimets, P.; Golub, L.; Madsen, C. A.; Marquez, V.; Bryans, P.; Judge, P. G.; Lussier, L.; McIntosh, S. W.; Tomczyk, S.

2017-12-01

Direct measurements of coronal magnetic fields are critical for taking the next step in active region and solar wind modeling and for building the next generation of physics-based space-weather models. We are proposing a new airborne instrument to make these key observations. Building on the successful Airborne InfraRed Spectrograph (AIR-Spec) experiment for the 2017 eclipse, we will design and build a spectro-polarimeter to measure coronal magnetic field during the 2019 South Pacific eclipse. The new instrument will use the AIR-Spec optical bench and the proven pointing, tracking, and stabilization optics. A new cryogenic spectro-polarimeter will be built focusing on the strongest emission lines observed during the eclipse. The AIR-Spec IR camera, slit jaw camera and data acquisition system will all be reused. The poster will outline the optical design and the science goals for ASPIRE.

High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

PubMed Central

Kim, Kyoohyun; Yoon, HyeOk; Diez-Silva, Monica; Dao, Ming; Dasari, Ramachandra R.

2013-01-01

Abstract. We present high-resolution optical tomographic images of human red blood cells (RBC) parasitized by malaria-inducing Plasmodium falciparum (Pf)-RBCs. Three-dimensional (3-D) refractive index (RI) tomograms are reconstructed by recourse to a diffraction algorithm from multiple two-dimensional holograms with various angles of illumination. These 3-D RI tomograms of Pf-RBCs show cellular and subcellular structures of host RBCs and invaded parasites in fine detail. Full asexual intraerythrocytic stages of parasite maturation (ring to trophozoite to schizont stages) are then systematically investigated using optical diffraction tomography algorithms. These analyses provide quantitative information on the structural and chemical characteristics of individual host Pf-RBCs, parasitophorous vacuole, and cytoplasm. The in situ structural evolution and chemical characteristics of subcellular hemozoin crystals are also elucidated. PMID:23797986

The use of enzymopathic human red cells in the study of malarial parasite glucose metabolism.

PubMed

Roth, E; Joulin, V; Miwa, S; Yoshida, A; Akatsuka, J; Cohen-Solal, M; Rosa, R

1988-05-01

The in vitro growth of Plasmodium falciparum malaria parasites was assayed in mutant red cells deficient in either diphosphoglycerate mutase (DPGM) or phosphoglycerate kinase (PGK). In addition, cDNA probes developed for human DNA sequences coding for these enzymes were used to examine the parasite genome by means of restriction endonuclease digestion and Southern blot analysis of parasite DNA. In both types of enzymopathic red cells, parasite growth was normal. In infected DPGM deficient red cells, no DPGM activity could be detected, and in normal red cells, DPGM activity declined slightly in a manner suggestive of parasite catabolism of host protein. However, in infected PGK deficient red cells, there was a 100-fold increase in PGK activity, and in normal red cells, a threefold increase in PGK activity was observed. Parasite PGK could be recovered from isolated parasites, and a marked increase in heat instability of parasite PGK as compared with the host cell enzyme was noted. Neither cDNA probe was found to cross-react with DNA sequences in the parasite genome. It is concluded that the parasite has no requirement for DPGM, and probably has no gene for this enzyme. On the other hand, the parasite does require PGK, (an adenosine triphosphate [ATP] generating enzyme) and synthesizes its own enzyme, which must have been encoded in the parasite genome. The parasite PGK gene most likely lacks sufficient homology to be detected by a human cDNA probe. Enzymopathic red cells are useful tools for elucidating the glycolytic enzymology of parasites and their co-evolution with their human hosts.

Rapid identification of pathogenic streptococci isolated from moribund red tilapia (Oreochromis spp.).

PubMed

Abdelsalam, Mohamed; Elgendy, Mamdouh Y; Shaalan, Mohamed; Moustafa, Mohamed; Fujino, Masayuki

2017-03-01

Accurate and rapid identification of bacterial pathogens of fish is essential for the effective treatment and speedy control of infections. Massive mortalities in market-sized red tilapia (Oreochromis spp.) were noticed in mariculture concrete ponds in northern Egypt. Histopathological examination revealed marked congestion in the central vein of the liver with the presence of bacterial aggregates inside the lumen and in the vicinity of the central vein. A total of 12 isolates of streptococci were obtained from the moribund fish. This study documented the ability of the MicroSeq 500 16S bacterial sequencing method to accurately identify Streptococcus agalactiae and S. dysgalactiae mixed infections from moribund red tilapia that were difficult to be recognised by the commercial biochemical systems. The continuously decreasing cost of the sequencing technique should encourage its application in routine diagnostic procedures.

VizieR Online Data Catalog: Optically red galaxies in H-ATLAS/GAMA (Dariush+, 2016)

NASA Astrophysics Data System (ADS)

Dariush, A.; Dib, S.; Hony, S.; Smith, D. J. B.; Zhukovska, S.; Dunne, L.; Eales, S.; Andrae, E.; Baes, M.; Baldry, I.; Bauer, A.; Bland-Hawthorn, J.; Brough, S.; Bourne, N.; Cava, A.; Clements, D.; Cluver, M.; Cooray, A.; de Zotti, G.; Driver, S.; Grootes, M. W.; Hopkins, A. M.; Hopwood, R.; Kaviraj, S.; Kelvin, L.; Lara-Lopez, M. A.; Liske, J.; Loveday, J.; Maddox, S.; Madore, B.; Michalowski, M. J.; Pearson, C.; Popescu, C.; Robotham, A.; Rowlands, K.; Seibert, M.; Shabani, F.; Smith, M. W. L.; Taylor, E. N.; Tuffs, R.; Valiante, E.; Virdee, J. S.

2016-09-01

We use data from the H-ATLAS phase 1 version 3.0 internal release which contains the IDs of >5σ SPIRE detections at 250um. We define two sub-samples of red and blue galaxies based on NUV-r colours. The morphology of all 117 red galaxies were examined from their SDSS r-band images, following independent visual inspection by three team members. Galaxies were classified into three categories of elliptical (E), spiral (S) and uncertain (U). (2 data files).

Intravital Confocal and Two-photon Imaging of Dual-color Cells and Extracellular Matrix Mimics

PubMed Central

Bal, Ufuk; Andresen, Volker; Baggett, Brenda; Utzinger, Urs

2013-01-01

To optimize imaging of cells in three dimensional culture we studied confocal backscattering, Second Harmonic Generation (SHG) and autofluorescence as source of contrast in extracellular matrix (ECM) mimics and evaluated the attenuation as well as bleaching of endogenous cellular fluorescence signals. All common ECM mimics exhibit contrast observable with confocal reflectance microscopy. SHG imaging on collagen I based hydrogels provides high contrast and good optical penetration depth. Agarose is a useful embedding medium because it allows for large optical penetration and exhibits minimal autofluorescence while still providing good reflectance to detect voids in the embedding medium. We labeled breast cancer cells’ outline with DsRed2 and nucleus with eGFP. DsRed2 can be excited with confocal imaging at 568nm, and with two photon excitation (TPE) in the red and longer NIR. eGFP was excited at 488nm for confocal and in the NIR for TPE. While there is small difference in the bleaching rate for eGFP between confocal and TPE we observed significant difference for DsRed2 where bleaching is strongest during TPE in the red wavelengths and smallest during confocal imaging. After a few hundred microns depth in a collagen I hydrogel, TPE fluorescence becomes twice as strong compared to confocal imaging. PMID:23380006

Fluorescence and Nonlinear Optical Properties of Alizarin Red S in Solvents and Droplet.

PubMed

Sangsefedi, Seyed Ahmad; Sharifi, Soheil; Rezaion, Hadi Rastegar Moghaddam; Azarpour, Afshin

2018-05-28

The enhancement of the nonlinear properties of materials is an interesting topic since it has many applications in optical devices and medicines. The Z-scan technique was used to study the values of the two-photon absorption (β), second-order molecular hyperpolarizability (γ R ), third-order susceptibility (χ R ), and nonlinear refractive index (n 2 ) of Alizarin Red S in different media using a continuous-wave diode-pump laser radiation at 532 nm. For Alizarin Red S in a droplet, the β, n 2 , χ R, and γ R were estimated at the order of 10 -7  cm 2 /W and 10 -12  cm/W, 10 -3  m 3  W -1  s -1 and 10 -24  m 6  W -1  s -1 , respectively. The results indicated that the values of β and n 2 reduced, whereas the values of χ R and γ R were enhanced when the solvent was changed from droplet to water, DMF, and dimethyl sulfoxide due to the change in the solvent's dielectric constant (ε). Moreover, the values of β were enhanced by an increase in the concentration of the surfactant in the aqueous solution. The absorption spectra of Alizarin Red S in the aqueous solution was observed at 428 nm, and a few red shifts in the absorption spectra were observed with a reduction in the dielectric constant of the medium. The same effect was observed in the absorption spectra of Alizarin Red S in the droplet when the bulk dielectric constant reduced. The dielectric constant can affect the fluorescence spectra of Alizarin Red S when the solution is changed from water to dimethyl sulfoxide. The dipole moments of Alizarin Red S in the different media were studied using the quantum perturbation theory.

Comparison between mixed and spatially separated remote phosphor fabricated via a screen-printing process

NASA Astrophysics Data System (ADS)

Kim, Byung-Ho; Hwang, Jonghee; Lee, Young Jin; Kim, Jin-Ho; Jeon, Dae-Woo; Lee, Mi Jai

2016-08-01

We developed a fabrication method for remote phosphor by a screen-printing process, using green phosphor, red phosphor, and thermally stable glass frit. The glass frit was introduced for long-term stability. The optical properties of the remote phosphor were observed via an integrating sphere; the photoluminescence spectrum dramatically changed on incorporating a minor amount of the red phosphor. These unique optical properties were elucidated using four factors: phosphor ratio, scattering induced by packing density, light intensity per unit volume, and reabsorption. The thermal stability of the remote phosphor was investigated at 500°C, demonstrating its outstanding thermal properties.

Light comfort zones of mesopelagic acoustic scattering layers in two contrasting optical environments

NASA Astrophysics Data System (ADS)

Røstad, Anders; Kaartvedt, Stein; Aksnes, Dag L.

2016-07-01

We make a comparison of the mesopelagic sound scattering layers (SLs) in two contrasting optical environments; the clear Red Sea and in murkier coastal waters of Norway (Masfjorden). The depth distributions of the SL in Masfjorden are shallower and narrower than those of the Red Sea. This difference in depth distribution is consistent with the hypothesis that the organisms of the SL distribute according to similar light comfort zones (LCZ) in the two environments. Our study suggest that surface and underwater light measurements ranging more than 10 orders of magnitude is required to assess the controlling effects of light on SL structure and dynamics.

Measurement of elastic light scattering from two optically trapped microspheres and red blood cells in a transparent medium.

PubMed

Kinnunen, Matti; Kauppila, Antti; Karmenyan, Artashes; Myllylä, Risto

2011-09-15

Optical tweezers can be used to manipulate small objects and cells. A trap can be used to fix the position of a particle during light scattering measurements. The places of two separately trapped particles can also be changed. In this Letter we present elastic light scattering measurements as a function of scattering angle when two trapped spheres are illuminated with a He-Ne laser. This setup is suitable for trapping noncharged homogeneous spheres. We also demonstrate measurement of light scattering patterns from two separately trapped red blood cells. Two different illumination schemes are used for both samples.

Red, green and blue reflections enabled in an optically tunable self-organized 3D cubic nanostructured thin film.

PubMed

Lin, Tsung-Hsien; Li, Yannian; Wang, Chun-Ta; Jau, Hung-Chang; Chen, Chun-Wei; Li, Cheng-Chung; Bisoyi, Hari Krishna; Bunning, Timothy J; Li, Quan

2013-09-25

A new light-driven chiral molecular switch doped in a stable blue phase (BP) liquid crystal allows wide optical tunability of three-dimensional cubic nanostructures with a selective reflection wavelength that is reversibly tuned through the visible region. Moreover, unprecedented reversible light-directed red, green, and blue reflections of the self-organized three-dimensional cubic nanostructure in a single film are demonstrated for the first time. Additionally, unusual isothermal photo-stimulated less ordered BP II to more ordered BP I phase transition was observed in the system. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of a red diode laser system for photodynamic therapy

NASA Astrophysics Data System (ADS)

Halkiotis, Konstantinos N.; Yova, Dido M.; Uzunoglou, Nikolaos K.; Papastergiou, Georgios; Matakias, Sotiris; Koukouvinos, Ilias

1998-07-01

The effectiveness of photodynamic treatment modality has been proven experimentally for a large variety of tumors, during the last years. This therapy utilizes the combined action of light and photosensitizing drug. Until now, a disadvantage of PDT has be the low tissue penetration of light, at the wavelengths of most commonly available lasers, for clinical studies. The red wavelength offers the advantage of increased penetration depth in tissue, in addition several new wavelength offers the advantage of increased penetration depth in tissue, in addition several new photosensitizers present absorption band at the region 630nm to 690nm. The development of high power red diode laser system for photodynamic therapy, has provided a cost effective alternative to existing lasers for use in PDT. This paper will describe the system design, development and performance of a diode laser system, connected with a fiber optic facility, to be used for PDT. The system was based on a high power semiconductor diode laser emitting at 655nm. The laser output power was approximately 60mW at the output of a 62.5/125/900 micron fiber optic probe. FUll technical details and optical performance characteristics of the system will be discussed in this paper.

Optical Processing Techniques For Pseudorandom Sequence Prediction

NASA Astrophysics Data System (ADS)

Gustafson, Steven C.

1983-11-01

Pseudorandom sequences are series of apparently random numbers generated, for example, by linear or nonlinear feedback shift registers. An important application of these sequences is in spread spectrum communication systems, in which, for example, the transmitted carrier phase is digitally modulated rapidly and pseudorandomly and in which the information to be transmitted is incorporated as a slow modulation in the pseudorandom sequence. In this case the transmitted information can be extracted only by a receiver that uses for demodulation the same pseudorandom sequence used by the transmitter, and thus this type of communication system has a very high immunity to third-party interference. However, if a third party can predict in real time the probable future course of the transmitted pseudorandom sequence given past samples of this sequence, then interference immunity can be significantly reduced.. In this application effective pseudorandom sequence prediction techniques should be (1) applicable in real time to rapid (e.g., megahertz) sequence generation rates, (2) applicable to both linear and nonlinear pseudorandom sequence generation processes, and (3) applicable to error-prone past sequence samples of limited number and continuity. Certain optical processing techniques that may meet these requirements are discussed in this paper. In particular, techniques based on incoherent optical processors that perform general linear transforms or (more specifically) matrix-vector multiplications are considered. Computer simulation examples are presented which indicate that significant prediction accuracy can be obtained using these transforms for simple pseudorandom sequences. However, the useful prediction of more complex pseudorandom sequences will probably require the application of more sophisticated optical processing techniques.

Optical properties of Si+ implanted PMMA

NASA Astrophysics Data System (ADS)

Balabanov, S.; Tsvetkova, T.; Borisova, E.; Avramov, L.; Bischoff, L.; Zuk, J.

2010-04-01

In the present work, low energy ion beam irradiation was used for surface modification of polymethyl-methacrylate (PMMA) using silicon (Si+) as the ion species. After high doses ion implantation of Si+ in the polymer material, a characterization of the optical properties was performed using optical transmission measurements in the visible and near infra-red (IR) wavelength range. The optical absorption increase observed with the ion dose was attributed to ion beam induced structural changes in the modified material.

High spectral resolution spectroscopy of the SiO fundamental lines in red giants and red supergiants with VLT/VISIR

NASA Astrophysics Data System (ADS)

Ohnaka, K.

2014-01-01

Context. The mass-loss mechanism in red giants and red supergiants is not yet understood well. The SiO fundamental lines near 8 μm are potentially useful for probing the outer atmosphere, which is essential for clarifying the mass-loss mechanism. However, these lines have been little explored until now. Aims: We present high spectral resolution spectroscopic observations of the SiO fundamental lines near 8.1 μm in 16 bright red giants and red supergiants. Our sample consists of seven normal (i.e., non-Mira) K-M giants (from K1.5 to M6.5), three Mira stars, three optically bright red supergiants, two dusty red supergiants, and the enigmatic object GCIRS3 near the Galactic center. Methods: Our program stars were observed between 8.088 μm and 8.112 μm with a spectral resolution of 30 000 using VLT/VISIR. Results: We detected SiO fundamental lines in all of our program stars except for GCIRS3. The SiO lines in normal K and M giants as well as optically bright (i.e., not dusty) red supergiants do not show P-Cyg profiles or blueshifts, which means the absence of systematic outflows in the SiO line forming region. We detected P-Cyg profiles in the SiO lines in the dusty red supergiants VY CMa and VX Sgr, with the latter object being a new detection. These SiO lines originate in the outflowing gas with the thermal dust continuum emission seen as the background. The outflow velocities of the SiO line forming region in VY CMa and VX Sgr are estimated to be 27 km s-1 and 17 km s-1, respectively. We derived basic stellar parameters (effective temperature, surface gravity, luminosity, and mass) for the normal K-M giants and optically bright red supergiants in our sample and compared the observed VISIR spectra with synthetic spectra predicted from MARCS photospheric models. Most of the SiO lines observed in the program stars warmer than ~3400 K are reasonably reproduced by the MARCS models, which allowed us to estimate the silicon abundance as well as the 28Si/29Si and 28Si/30Si ratios. However, we detected possible absorption excess in some SiO lines. Moreover, the SiO lines in the cooler red giants and red supergiant cannot be explained by the MARCS models at all, even if the dust emission is taken into account. This disagreement may be a signature of the dense, extended molecular outer atmosphere. Based on VISIR observations made with the Very Large Telescope of the European Southern Observatory. Program ID: 087.D-0522(A).Reduced spectra are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/561/A47

TOF-SIMS Analysis of Red Color Inks of Writing and Printing Tools on Questioned Documents.

PubMed

Lee, Jihye; Nam, Yun Sik; Min, Jisook; Lee, Kang-Bong; Lee, Yeonhee

2016-05-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a well-established surface technique that provides both elemental and molecular information from several monolayers of a sample surface while also allowing depth profiling or image mapping to be performed. Static TOF-SIMS with improved performances has expanded the application of TOF-SIMS to the study of a variety of organic, polymeric, biological, archaeological, and forensic materials. In forensic investigation, the use of a minimal sample for the analysis is preferable. Although the TOF-SIMS technique is destructive, the probing beams have microsized diameters so that only small portion of the questioned sample is necessary for the analysis, leaving the rest available for other analyses. In this study, TOF-SIMS and attenuated total reflectance Fourier transform infrared (ATR-FTIR) were applied to the analysis of several different pen inks, red sealing inks, and printed patterns on paper. The overlapping areas of ballpoint pen writing, red seal stamping, and laser printing in a document were investigated to identify the sequence of recording. The sequence relations for various cases were determined from the TOF-SIMS mapping image and the depth profile. TOF-SIMS images were also used to investigate numbers or characters altered with two different red pens. TOF-SIMS was successfully used to determine the sequence of intersecting lines and the forged numbers on the paper. © 2016 American Academy of Forensic Sciences.

Development of a codon optimization strategy using the efor RED reporter gene as a test case

NASA Astrophysics Data System (ADS)

Yip, Chee-Hoo; Yarkoni, Orr; Ajioka, James; Wan, Kiew-Lian; Nathan, Sheila

2018-04-01

Synthetic biology is a platform that enables high-level synthesis of useful products such as pharmaceutically related drugs, bioplastics and green fuels from synthetic DNA constructs. Large-scale expression of these products can be achieved in an industrial compliant host such as Escherichia coli. To maximise the production of recombinant proteins in a heterologous host, the genes of interest are usually codon optimized based on the codon usage of the host. However, the bioinformatics freeware available for standard codon optimization might not be ideal in determining the best sequence for the synthesis of synthetic DNA. Synthesis of incorrect sequences can prove to be a costly error and to avoid this, a codon optimization strategy was developed based on the E. coli codon usage using the efor RED reporter gene as a test case. This strategy replaces codons encoding for serine, leucine, proline and threonine with the most frequently used codons in E. coli. Furthermore, codons encoding for valine and glycine are substituted with the second highly used codons in E. coli. Both the optimized and original efor RED genes were ligated to the pJS209 plasmid backbone using Gibson Assembly and the recombinant DNAs were transformed into E. coli E. cloni 10G strain. The fluorescence intensity per cell density of the optimized sequence was improved by 20% compared to the original sequence. Hence, the developed codon optimization strategy is proposed when designing an optimal sequence for heterologous protein production in E. coli.

The Study of Upper Ocean Stratification that Controls Propagation of Internal Tidal Bores in Coastal Areas

DTIC Science & Technology

2012-06-01

turbulence . McPhee-Shaw determined that intrusions typically formed in regions where the incident and reflected wave beams overlap on the slope...Figure 7. Optical backscatter data from the Spray glider. The saturation point for the optical backscatter is 4.096 V. The green and red profiles...plot is a cross shelf section of optical backscatter . ..........................................................................25 Figure 9

Melanin deposition ruled out as cause of color changes in the red-eared sliders (Trachemys scripta elegans).

PubMed

Cao, Dainan; Gong, Shiping; Yang, Jiangbo; Li, Weiye; Ge, Yan; Wei, Yufeng

2018-03-01

Animal coloration primarily depends on the presence of pigments and the mixing ratio of eumelanin and pheomelanin. The color of red-eared slider's carapace varies with age, from an olive green to a yellow green, and then to a yellow brown in juveniles, generally. The purpose of the present study was to investigate whether this color change is related to the difference in melanin expression. Melanin deposition levels were examined in the carapace, skin, eye and muscle of the three color-types using hematoxylin and eosin staining. Moreover, the full-length coding sequence (CDS) of red-eared slider turtle melanin biosynthesis regulatory genes TYR, TYRP1, MITF and SLC24A5 were cloned, sequenced and quantitatively analyzed. Both histological view of melanin deposition and quantitative real-time PCR test of melanin-regulated gene expressions showed that there are significant differences among different tissues of red-eared slider, but no significant difference among different color-types, indicating that melanin deposition is not associated with ontogenetic color change in the carapace of red-eared slider. This study initially explore the melanin deposition and the mRNA expression of melanin biosynthesis regulatory genes in red-eared slider, which serve as a foundation for further insight into the pigmentation patterns and the mechanism of body color change in turtles. Copyright © 2017 Elsevier Inc. All rights reserved.

The star forming universe after z=1

NASA Astrophysics Data System (ADS)

Harker, Justin J.

This dissertation explores three projects in the field of galaxy formation and evolution: the formation of the red sequence via quenching, the detection, characterization, and frequency of starbursts in the DEEP2 sample, and the behavior of a main sequence of star forming galaxies whose behavior is determined by baryonic mass, referred to as staged star formation. The first section, in Chapter 2, presents a breakdown of several population synthesis models designed to probe the history of the red sequence. Known from measurements at low redshift to be composed of objects with a large range of ages, the red sequence is not well-modeled as being the result of a single monolithic event in the distant past. By combining information on restframe color, Balmer absorption line strengths, and the number density of L* galaxies as a function of redshift, we find evidence that the red sequence is built up over time. The second section, in Chapter 3 and 4, presents a novel method for determining simultaneously the absorption line and emission line contributions to the total measured equivalent width of Balmer lines. Relying on the predictable behavior of both absorption lines, which are to first order equivalent to one another, and emission lines, which follow a predictable decrement toward shorter wavelengths, a single measurement of total line strength for Hb and Hd yield uncoupled emission and absorption line components. Using the measurement of Hd in absorption against D n 4000 and Hb in emission, we isolate a population of potential starbursts in the DEEP2 sample. The final section, in Chapter 5, explores the regularity of star formation as a function of redshift, using the staged star formation prescription of Noeske et al. (2007a). We compute a set of t-models using the prescription, and compare them to the data in a number of parameters in addition to mass and star formation. While the staged star formation model is a good match in a number of parameters, we find several irregularities.

A molecular survey of Babesia spp. and Theileria spp. in red foxes (Vulpes vulpes) and their ticks from Thuringia, Germany.

PubMed

Najm, Nour-Addeen; Meyer-Kayser, Elisabeth; Hoffmann, Lothar; Herb, Ingrid; Fensterer, Veronika; Pfister, Kurt; Silaghi, Cornelia

2014-06-01

Wild canines which are closely related to dogs constitute a potential reservoir for haemoparasites by both hosting tick species that infest dogs and harbouring tick-transmitted canine haemoparasites. In this study, the prevalence of Babesia spp. and Theileria spp. was investigated in German red foxes (Vulpes vulpes) and their ticks. DNA extracts of 261 spleen samples and 1953 ticks included 4 tick species: Ixodes ricinus (n=870), I. canisuga (n=585), I. hexagonus (n=485), and Dermacentor reticulatus (n=13) were examined for the presence of Babesia/Theileria spp. by a conventional PCR targeting the 18S rRNA gene. One hundred twenty-one out of 261 foxes (46.4%) were PCR-positive. Out of them, 44 samples were sequenced, and all sequences had 100% similarity to Theileria annae. Similarly, sequencing was carried out for 65 out of 118 PCR-positive ticks. Theileria annae DNA was detected in 61.5% of the sequenced samples, Babesia microti DNA was found in 9.2%, and Babesia venatorum in 7.6% of the sequenced samples. The foxes were most positive in June and October, whereas the peak of tick positivity was in October. Furthermore, the positivity of the ticks was higher for I. canisuga in comparison to the other tick species and for nymphs in comparison to adults. The high prevalence of T. annae DNA in red foxes in this study suggests a reservoir function of those animals for T. annae. To our knowledge, this is the first report of T. annae in foxes from Germany as well as the first detection of T. annae and B. microti in the fox tick I. canisuga. Detection of DNA of T. annae and B. microti in three tick species collected from foxes adds new potential vectors for these two pathogens and suggests a potential role of the red fox in their natural endemic cycles. Copyright © 2014 Elsevier GmbH. All rights reserved.

Simulation of the Pinatubo Impact on the Red Sea Using Coupled Regional Ocean/Atmosphere Modeling System

NASA Astrophysics Data System (ADS)

Stenchikov, G. L.; Osipov, S.

2016-12-01

This study focuses on the Middle East regional climate response to the Mt. Pinatubo volcanic eruption of 1991. It is motivated by the observed severe winter cooling in the Middle East during the winter of 1991/92. The Red Sea surface temperature dropped by more than 1K and deep water mixing caused coral bleaching for a few years. To better understand the mechanisms of the Middle East climate response and evaluate the effects of radiative cooling and regional meteorological processes on the Red Sea, we employ the Regional Ocean Modeling system (ROMS) fully coupled with the Weather Research and Forecasting (WRF) model. The WRF model parent and nested domains are configured over the Middle East and North Africa (MENA) region and over the Red Sea with 30 and 10 km resolution, respectively. The ROMS model over the Red Sea has 2 km grid spacing. The WRF code was modified to interactively account for the radiative effect of volcanic aerosols. Spectral optical properties of sulfate aerosols are computed using Mie based on the Sato's optical depth. Both atmosphere and ocean models capture the main features of the MENA climate response and correctly reproduce the anomalous winter cooling of 1991/92. We find that the sea surface cooling associated with meteorological effects prevails that caused by the direct radiative forcing of volcanic aerosols. The overturning circulation in the Red Sea strengthens. The salinity distribution and deep water formation are significantly perturbed.

A clone-free, single molecule map of the domestic cow (Bos taurus) genome.

PubMed

Zhou, Shiguo; Goldstein, Steve; Place, Michael; Bechner, Michael; Patino, Diego; Potamousis, Konstantinos; Ravindran, Prabu; Pape, Louise; Rincon, Gonzalo; Hernandez-Ortiz, Juan; Medrano, Juan F; Schwartz, David C

2015-08-28

The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation. The optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts). Alignments of UMD3.1 and Btau4.6 to BtOM1.0 reveal discordances commensurate with previous reports, and affirm the NCBI's current designation of UMD3.1 sequence assembly as the "reference assembly" and the Btau4.6 as the "alternate assembly." The cattle genome optical map, BtOM1.0, when used as a comprehensive and largely independent guide, will greatly assist improvements to existing sequence builds, and later serve as an accurate physical scaffold for studies concerning the comparative genomics of cattle breeds.

Study on multiple-hops performance of MOOC sequences-based optical labels for OPS networks

NASA Astrophysics Data System (ADS)

Zhang, Chongfu; Qiu, Kun; Ma, Chunli

2009-11-01

In this paper, we utilize a new study method that is under independent case of multiple optical orthogonal codes to derive the probability function of MOOCS-OPS networks, discuss the performance characteristics for a variety of parameters, and compare some characteristics of the system employed by single optical orthogonal code or multiple optical orthogonal codes sequences-based optical labels. The performance of the system is also calculated, and our results verify that the method is effective. Additionally it is found that performance of MOOCS-OPS networks would, negatively, be worsened, compared with single optical orthogonal code-based optical label for optical packet switching (SOOC-OPS); however, MOOCS-OPS networks can greatly enlarge the scalability of optical packet switching networks.

The Mid-infrared View of Red Sequence Galaxies in Abell 2218 with AKARI

NASA Astrophysics Data System (ADS)

Ko, Jongwan; Im, Myungshin; Lee, Hyung Mok; Lee, Myung Gyoon; Hopwood, Ros H.; Serjeant, Stephen; Smail, Ian; Hwang, Ho Seong; Hwang, Narae; Shim, Hyunjin; Kim, Seong Jin; Lee, Jong Chul; Lim, Sungsoon; Seo, Hyunjong; Goto, Tomotsugu; Hanami, Hitoshi; Matsuhara, Hideo; Takagi, Toshinobu; Wada, Takehiko

2009-04-01

We present the AKARI Infrared Camera (IRC) imaging observation of early-type galaxies (ETGs) in A2218 at zsime 0.175. Mid-infrared (MIR) emission from ETGs traces circumstellar dust emission from asymptotic giant branch (AGB) stars or/and residual star formation. Including the unique imaging capability at 11 and 15 μm, our AKARI data provide an effective way to investigate MIR properties of ETGs in the cluster environment. Among our flux-limited sample of 22 red sequence ETGs with precise dynamical and line strength measurements (less than 18 mag at 3 μm), we find that at least 41% have MIR-excess emission. The N3 - S11 versus N3 (3 and 11 μm) color-magnitude relation shows the expected blue sequence, but the MIR-excess galaxies add a red wing to the relation especially at the fainter end. A spectral energy distribution analysis reveals that the dust emission from AGB stars is the most likely cause of the MIR excess, with a low level of star formation being the next possible explanation. The MIR-excess galaxies show a wide spread of N3 - S11 colors, implying a significant spread (2-11 Gyr) in the estimated mean ages of stellar populations. We study the environmental dependence of MIR-excess ETGs over an area out to a half virial radius (~1 Mpc). We find that the MIR-excess ETGs are preferentially located in the outer region. From this evidence, we suggest that the fainter, MIR-excess ETGs have just joined the red sequence, possibly due to the infall and subsequent morphological/spectral transformation induced by the cluster environment.

Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants.

PubMed

Iso-Touru, T; Sahana, G; Guldbrandtsen, B; Lund, M S; Vilkki, J

2016-03-22

The Nordic Red Cattle consisting of three different populations from Finland, Sweden and Denmark are under a joint breeding value estimation system. The long history of recording of production and health traits offers a great opportunity to study production traits and identify causal variants behind them. In this study, we used whole genome sequence level data from 4280 progeny tested Nordic Red Cattle bulls to scan the genome for loci affecting milk, fat and protein yields. Using a genome-wise significance threshold, regions on Bos taurus chromosomes 5, 14, 23, 25 and 26 were associated with fat yield. Regions on chromosomes 5, 14, 16, 19, 20 and 25 were associated with milk yield and chromosomes 5, 14 and 25 had regions associated with protein yield. Significantly associated variations were found in 227 genes for fat yield, 72 genes for milk yield and 30 genes for protein yield. Ingenuity Pathway Analysis was used to identify networks connecting these genes displaying significant hits. When compared to previously mapped genomic regions associated with fertility, significantly associated variations were found in 5 genes common for fat yield and fertility, thus linking these two traits via biological networks. This is the first time when whole genome sequence data is utilized to study genomic regions affecting milk production in the Nordic Red Cattle population. Sequence level data offers the possibility to study quantitative traits in detail but still cannot unambiguously reveal which of the associated variations is causative. Linkage disequilibrium creates difficulties to pinpoint the causative genes and variations. One solution to overcome these difficulties is the identification of the functional gene networks and pathways to reveal important interacting genes as candidates for the observed effects. This information on target genomic regions may be exploited to improve genomic prediction.

Initiation and Along-Axis Segmentation of Seaward-Dipping Volcanic Sequences Captured in Afar

NASA Astrophysics Data System (ADS)

Ebinger, C.; Wolfenden, E.; Yirgu, G.; Keir, D.

2003-12-01

The Afar triple junction zone provides a unique opportunity to examine the early development of magmatic margins, as respective limbs of the triple junction capture different stages of the breakup process. Initial rifting in the southernmost Red Sea occurred concurrent with, or soon after flood basaltic magmatism at ~31 Ma in the Ethiopia-Yemen plume province, whereas the northern part of the Main Ethiopian rift initiated after 12 Ma. Both rift systems initiated with the development of high-angle border fault systems bounding broad basins, but 8-10 My after rifting we see riftward migration of strain from the western border fault to narrow zones of increasingly more basaltic magmatism. These localised zones of faulting and volcanism (magmatic segments) show a segmentation independent of the border fault segmentation. The much older, more evolved magmatic segments in the southern Red Sea, where not onlapped by Pliocene-Recent sedimentary strata, dip steeply riftward and define a regional eastward flexure into transitional oceanic crust, as indicated by gravity models constrained by seismic refraction and receiver function data. The southern Red Sea magmatic segments have been abandoned in Pliocene-Recent triple junction reorganisations, whereas the process of seaward-dipping volcanic sequence emplacement is ongoing in the seismically and volcanically active Main Ethiopian rift. Field, remote sensing, gravity, and seismicity data from the Main Ethiopian and southern Red Sea rifts indicate that seaward-dipping volcanic sequences initiate in moderately stretched continental crust above a narrow zone of dike-intrusion. Our comparison of active and ancient magmatic segments show that they are the precursors to seaward-dipping volcanic sequences analogous to those seen on passive continental margins, and provides insights into the initiation of along-axis segmentation of seafloor-spreading centers.

Color-magnitude distribution of face-on nearby galaxies in Sloan digital sky survey DR7

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

Jin, Shuo-Wen; Feng, Long-Long; Gu, Qiusheng

2014-05-20

We have analyzed the distributions in the color-magnitude diagram (CMD) of a large sample of face-on galaxies to minimize the effect of dust extinctions on galaxy color. About 300,000 galaxies with log (a/b) < 0.2 and redshift z < 0.2 are selected from the Sloan Digital Sky Survey DR7 catalog. Two methods are employed to investigate the distributions of galaxies in the CMD, including one-dimensional (1D) Gaussian fitting to the distributions in individual magnitude bins and two-dimensional (2D) Gaussian mixture model (GMM) fitting to galaxies as a whole. We find that in the 1D fitting, two Gaussians are not enoughmore » to fit galaxies with the excess present between the blue cloud and the red sequence. The fitting to this excess defines the center of the green valley in the local universe to be (u – r){sub 0.1} = –0.121M {sub r,} 0{sub .1} – 0.061. The fraction of blue cloud and red sequence galaxies turns over around M {sub r,} {sub 0.1} ∼ –20.1 mag, corresponding to stellar mass of 3 × 10{sup 10} M {sub ☉}. For the 2D GMM fitting, a total of four Gaussians are required, one for the blue cloud, one for the red sequence, and the additional two for the green valley. The fact that two Gaussians are needed to describe the distributions of galaxies in the green valley is consistent with some models that argue for two different evolutionary paths from the blue cloud to the red sequence.« less

Co-infection and cross-species transmission of divergent Hepatocystis lineages in a wild African primate community.

PubMed

Thurber, Mary I; Ghai, Ria R; Hyeroba, David; Weny, Geoffrey; Tumukunde, Alex; Chapman, Colin A; Wiseman, Roger W; Dinis, Jorge; Steeil, James; Greiner, Ellis C; Friedrich, Thomas C; O'Connor, David H; Goldberg, Tony L

2013-07-01

Hemoparasites of the apicomplexan family Plasmodiidae include the etiological agents of malaria, as well as a suite of non-human primate parasites from which the human malaria agents evolved. Despite the significance of these parasites for global health, little information is available about their ecology in multi-host communities. Primates were investigated in Kibale National Park, Uganda, where ecological relationships among host species are well characterized. Blood samples were examined for parasites of the genera Plasmodium and Hepatocystis using microscopy and PCR targeting the parasite mitochondrial cytochrome b gene, followed by Sanger sequencing. To assess co-infection, "deep sequencing" of a variable region within cytochrome b was performed. Out of nine black-and-white colobus (Colobus guereza), one blue guenon (Cercopithecus mitis), five grey-cheeked mangabeys (Lophocebus albigena), 23 olive baboons (Papio anubis), 52 red colobus (Procolobus rufomitratus) and 12 red-tailed guenons (Cercopithecus ascanius), 79 infections (77.5%) were found, all of which were Hepatocystis spp. Sanger sequencing revealed 25 different parasite haplotypes that sorted phylogenetically into six species-specific but morphologically similar lineages. "Deep sequencing" revealed mixed-lineage co-infections in baboons and red colobus (41.7% and 64.7% of individuals, respectively) but not in other host species. One lineage infecting red colobus also infected baboons, but always as the minor variant, suggesting directional cross-species transmission. Hepatocystis parasites in this primate community are a diverse assemblage of cryptic lineages, some of which co-infect hosts and at least one of which can cross primate species barriers. Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Signatures of adaptation in the weedy rice genome

USDA-ARS?s Scientific Manuscript database

Weedy rice is a common problem of by product of domestication that has evolved multiple times from cultivated and wild rice relatives. Here we use whole genome sequences to examine the origin and adaptation of the two major US weedy red rice strains, with a comparison to Chinese weedy red rice. We f...

The Fate of Exoplanets and the Red Giant Rapid Rotator Connection

NASA Astrophysics Data System (ADS)

Carlberg, Joleen K.; Majewski, Steven R.; Arras, Phil; Smith, Verne V.; Cunha, Katia; Bizyaev, Dmitry

2011-03-01

We have computed the fate of exoplanet companions around main sequence stars to explore the frequency of planet ingestion by their host stars during the red giant branch evolution. Using published properties of exoplanetary systems combined with stellar evolution models and Zahn's theory of tidal friction, we modeled the tidal decay of the planets' orbits as their host stars evolve. Most planets currently orbiting within 2 AU of their star are expected to be ingested by the end of their stars' red giant branch ascent. Our models confirm that many transiting planets are sufficiently close to their parent star that they will be accreted during the main sequence lifetime of the star. We also find that planet accretion may play an important role in explaining the mysterious red giant rapid rotators, although appropriate planetary systems do not seem to be plentiful enough to account for all such rapid rotators. We compare our modeled rapid rotators and surviving planetary systems to their real-life counterparts and discuss the implications of this work to the broader field of exoplanets.

Full-length genome sequence of a simian immunodeficiency virus (SIV) infecting a captive agile mangabey (Cercocebus agilis) is closely related to SIVrcm infecting wild red-capped mangabeys (Cercocebus torquatus) in Cameroon

PubMed Central

Ahuka-Mundeke, Steve; Liegeois, Florian; Ayouba, Ahidjo; Foupouapouognini, Yacouba; Nerrienet, Eric; Delaporte, Eric; Peeters, Martine

2010-01-01

Simian immunodeficiency viruses (SIVs) are lentiviruses that infect an extensive number of wild African primate species. Here we describe for the first time SIV infection in a captive agile mangabey (Cercocebus agilis) from Cameroon. Phylogenetic analysis of the full-length genome sequence of SIVagi-00CM312 showed that this novel virus fell into the SIVrcm lineage and was most closely related to a newly characterized SIVrcm strain (SIVrcm-02CM8081) from a wild-caught red-capped mangabey (Cercocebus torquatus) from Cameroon. In contrast to red-capped mangabeys, no 24 bp deletion in CCR5 has been observed in the agile mangabey. Further studies on wild agile mangabeys are needed to determine whether agile and red-capped mangabeys are naturally infected with the same SIV lineage, or whether this agile mangabey became infected with an SIVrcm strain in captivity. However, our study shows that agile mangabeys are susceptible to SIV infection. PMID:20797968

Full-length genome sequence of a simian immunodeficiency virus (SIV) infecting a captive agile mangabey (Cercocebus agilis) is closely related to SIVrcm infecting wild red-capped mangabeys (Cercocebus torquatus) in Cameroon.

PubMed

Ahuka-Mundeke, Steve; Liegeois, Florian; Ayouba, Ahidjo; Foupouapouognini, Yacouba; Nerrienet, Eric; Delaporte, Eric; Peeters, Martine

2010-12-01

Simian immunodeficiency viruses (SIVs) are lentiviruses that infect an extensive number of wild African primate species. Here we describe for the first time SIV infection in a captive agile mangabey (Cercocebus agilis) from Cameroon. Phylogenetic analysis of the full-length genome sequence of SIVagi-00CM312 showed that this novel virus fell into the SIVrcm lineage and was most closely related to a newly characterized SIVrcm strain (SIVrcm-02CM8081) from a wild-caught red-capped mangabey (Cercocebus torquatus) from Cameroon. In contrast to red-capped mangabeys, no 24 bp deletion in CCR5 has been observed in the agile mangabey. Further studies on wild agile mangabeys are needed to determine whether agile and red-capped mangabeys are naturally infected with the same SIV lineage, or whether this agile mangabey became infected with an SIVrcm strain in captivity. However, our study shows that agile mangabeys are susceptible to SIV infection.

Bilateral optic disc drusen mimicking papilledema.

PubMed

Sahin, Alparslan; Cingü, Abdullah Kürşat; Ari, Seyhmus; Cinar, Yasin; Caça, Ihsan

2012-06-01

Optic disc drusen, which are calcified deposits that form anterior to the lamina cribrosa in the optic nerve, may mimic papilledema. We report herein three cases referred to us with suspicion of disc swelling and papilledema. Following ophthalmologic evaluation with B-scan ultrasound, red-free fundus photography, and computed tomography, the diagnosis of papilledema was excluded in all cases and optic disc drusen was diagnosed. Clinical suspicion of optic disc drusen in cases presenting with swelling of the optic nerve head is important in order to avoid unnecessary interventions and anxiety. The reported cases highlight the commonly encountered clinical presentations and the practical aspects of diagnosis and management of optic disc drusen.

Optical Communications Channel Combiner

NASA Technical Reports Server (NTRS)

Quirk, Kevin J.; Quirk, Kevin J.; Nguyen, Danh H.; Nguyen, Huy

2012-01-01

NASA has identified deep-space optical communications links as an integral part of a unified space communication network in order to provide data rates in excess of 100 Mb/s. The distances and limited power inherent in a deep-space optical downlink necessitate the use of photon-counting detectors and a power-efficient modulation such as pulse position modulation (PPM). For the output of each photodetector, whether from a separate telescope or a portion of the detection area, a communication receiver estimates a log-likelihood ratio for each PPM slot. To realize the full effective aperture of these receivers, their outputs must be combined prior to information decoding. A channel combiner was developed to synchronize the log-likelihood ratio (LLR) sequences of multiple receivers, and then combines these into a single LLR sequence for information decoding. The channel combiner synchronizes the LLR sequences of up to three receivers and then combines these into a single LLR sequence for output. The channel combiner has three channel inputs, each of which takes as input a sequence of four-bit LLRs for each PPM slot in a codeword via a XAUI 10 Gb/s quad optical fiber interface. The cross-correlation between the channels LLR time series are calculated and used to synchronize the sequences prior to combining. The output of the channel combiner is a sequence of four-bit LLRs for each PPM slot in a codeword via a XAUI 10 Gb/s quad optical fiber interface. The unit is controlled through a 1 Gb/s Ethernet UDP/IP interface. A deep-space optical communication link has not yet been demonstrated. This ground-station channel combiner was developed to demonstrate this capability and is unique in its ability to process such a signal.

Tomography of the Red Supergiant Star MU Cep

NASA Astrophysics Data System (ADS)

Kravchenko, Kateryna

2018-04-01

We present a tomographic method allowing to recover the velocity field at different optical depths in a stellar atmosphere. It is based on the computation of the contribution function to identify the depth of formation of spectral lines in order to construct numerical masks probing different optical depths. These masks are cross-correlated with observed spectra to extract information about the average shape of lines forming at a given optical depth and to derive the velocity field projected on the line of sight. We applied this method to series of spectra of the red supergiant star mu Cep and derived velocities in different atmospheric layers. The resulting velocity variations reveal complex atmospheric dynamics and indicate that convective cells are present in the atmosphere of the mu Cep. The mu Cep velocities were compared with those obtained by applying the tomographic masks to series of snapshot spectra from 3D radiative-hydrodynamics CO5BOLD simulations.

Euler buckling-induced folding and rotation of red blood cells in an optical trap

NASA Astrophysics Data System (ADS)

Ghosh, A.; Sinha, Supurna; Dharmadhikari, J. A.; Roy, S.; Dharmadhikari, A. K.; Samuel, J.; Sharma, S.; Mathur, D.

2006-03-01

We investigate the physics of an optically driven micromotor of biological origin. When a single, live red blood cell (RBC) is placed in an optical trap, the normal biconcave disc shape of the cell is observed to fold into a rod-like shape. If the trapping laser beam is circularly polarized, the folded RBC rotates. A model based on geometric considerations, using the concept of buckling instabilities, captures the folding phenomenon; the rotation of the cell is rationalized using the Poincaré sphere. Our model predicts that (i) at a critical power of the trapping laser beam the RBC shape undergoes large fluctuations, and (ii) the torque that is generated is proportional to the power of the laser beam. These predictions are verified experimentally. We suggest a possible mechanism for the emergence of birefringent properties in the RBC in the folded state.

Structural and optical studies on selected web spinning spider silks

NASA Astrophysics Data System (ADS)

Karthikeyani, R.; Divya, A.; Mathavan, T.; Asath, R. Mohamed; Benial, A. Milton Franklin; Muthuchelian, K.

2017-01-01

This study investigates the structural and optical properties in the cribellate silk of the sheet web spider Stegodyphus sarasinorum Karsch (Eresidae) and the combined dragline, viscid silk of the orb-web spiders Argiope pulchella Thorell (Araneidae) and Nephila pilipes Fabricius (Nephilidae). X-ray diffraction (XRD), Fourier transform infra-red (FTIR), Ultraviolet-visible (UV-Vis) and fluorescence spectroscopic techniques were used to study these three spider silk species. X-ray diffraction data are consistent with the amorphous polymer network which is arising from the interaction of larger side chain amino acid contributions due to the poly-glycine rich sequences known to be present in the proteins of cribellate silk. The same amorphous polymer networks have been determined from the combined dragline and viscid silk of orb-web spiders. From FTIR spectra the results demonstrate that, cribellate silk of Stegodyphus sarasinorum, combined dragline viscid silk of Argiope pulchella and Nephila pilipes spider silks are showing protein peaks in the amide I, II and III regions. Further they proved that the functional groups present in the protein moieties are attributed to α-helical and side chain amino acid contributions. The optical properties of the obtained spider silks such as extinction coefficients, refractive index, real and imaginary dielectric constants and optical conductance were studied extensively from UV-Vis analysis. The important fluorescent amino acid tyrosine is present in the protein folding was investigated by using fluorescence spectroscopy. This research would explore the protein moieties present in the spider silks which were found to be associated with α-helix and side chain amino acid contributions than with β-sheet secondary structure and also the optical relationship between the three different spider silks are investigated. Successful spectroscopic knowledge of the internal protein structure and optical properties of the spider silks could permit industrial production of silk-based fibres with unique properties under benign conditions.

The dark nemesis of galaxy formation: why hot haloes trigger black hole growth and bring star formation to an end

NASA Astrophysics Data System (ADS)

Bower, Richard G.; Schaye, Joop; Frenk, Carlos S.; Theuns, Tom; Schaller, Matthieu; Crain, Robert A.; McAlpine, Stuart

2017-02-01

Galaxies fall into two clearly distinct types: `blue-sequence' galaxies which are rapidly forming young stars, and `red-sequence' galaxies in which star formation has almost completely ceased. Most galaxies more massive than 3 × 1010 M⊙ follow the red sequence, while less massive central galaxies lie on the blue sequence. We show that these sequences are created by a competition between star formation-driven outflows and gas accretion on to the supermassive black hole at the galaxy's centre. We develop a simple analytic model for this interaction. In galaxies less massive than 3 × 1010 M⊙, young stars and supernovae drive a high-entropy outflow which is more buoyant than any tenuous corona. The outflow balances the rate of gas inflow, preventing high gas densities building up in the central regions. More massive galaxies, however, are surrounded by an increasingly hot corona. Above a halo mass of ˜1012 M⊙, the outflow ceases to be buoyant and star formation is unable to prevent the build-up of gas in the central regions. This triggers a strongly non-linear response from the black hole. Its accretion rate rises rapidly, heating the galaxy's corona, disrupting the incoming supply of cool gas and starving the galaxy of the fuel for star formation. The host galaxy makes a transition to the red sequence, and further growth predominantly occurs through galaxy mergers. We show that the analytic model provides a good description of galaxy evolution in the EAGLE hydrodynamic simulations. So long as star formation-driven outflows are present, the transition mass scale is almost independent of subgrid parameter choice.

Dopant concentration dependent optical and X-Ray induced photoluminescence in Eu3+ doped La2Zr2O7

NASA Astrophysics Data System (ADS)

Pokhrel, Madhab; Brik, Mikhail; Mao, Yuanbing

2015-03-01

Herein, we will be presenting the dopant (Eu) concentration dependent high density La2Zr2O7 nanoparticles for optical and X-ray scintillation applications by use of X - ray diffraction, Raman, FTIR, scanning electron microscope (SEM), transmission electron microscopy (TEM), optically and X-ray excited photoluminescence (PL). Several theoretical methods have been used in order to investigate the structural, electronic, optical, elastic, dynamic properties of Eu doped La2Zr2O7. It is observed that Eu: La2Zr2O7 shows an intense red luminescence under 258, 322, 394 and 465 nm excitation. The optical intensity of Eu: La2Zr2O7 depends on the dopant concentration of Eu3+. Following high energy excitation with X-rays, Eu: La2Zr2O7 shows an atypical Eu PL response (scintillation) with a red emission. The intense color emission of Eu obtained under 258 nm excitation, the X-ray induced luminescence property along with reportedly high density of La2Zr2O7, makes these nanomaterials attractive for optical and X-ray applications. The authors thank the support from the Defense Threat Reduction Agency (DTRA) of the U.S. Department of Defense (Award #HDTRA1-10-1-0114).

Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes.

PubMed

Kumar, Vikas; Kutschera, Verena E; Nilsson, Maria A; Janke, Axel

2015-08-07

The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species. The de novo assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago. Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic adaptation in foxes. Similar to polar bears, fat metabolism seems to play a central role in adaptation of Arctic foxes to the cold climate, as has been identified in the polar bear, another arctic specialist.

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method

PubMed Central

Xue, Huabai; Shi, Ting; Wang, Fangfang; Zhou, Huangkai; Yang, Jian; Wang, Long; Wang, Suke; Su, Yanli; Zhang, Zhen; Qiao, Yushan; Li, Xiugen

2017-01-01

Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the ‘Mantianhong’ and ‘Hongxiangsu’ red-skinned cultivars. The ‘Dangshansuli’ cultivar genome was used as reference for sequence alignment. An average single-nucleotide polymorphism (SNP) index was calculated using a sliding window approach (200-kb windows, 20-kb increments). Nine scaffolds within the candidate QTL interval were in the fifth linkage group from 111.9 to 177.1 cM. There was a significant linkage between the insertions/deletions and simple sequence repeat markers designed from the candidate intervals and the red/green skin (R/G) locus, which was in a 582.5-kb candidate interval that contained 81 predicted protein-coding gene models and was composed of two subintervals at the bottom of the fifth chromosome. The ZFRI 130-16, In2130-12 and In2130-16 markers located near the R/G locus could potentially be used to identify the red skin trait in Asian pear populations. This study provides new insights into the genetics controlling the red skin phenotype in this fruit. PMID:29118994

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method.

PubMed

Xue, Huabai; Shi, Ting; Wang, Fangfang; Zhou, Huangkai; Yang, Jian; Wang, Long; Wang, Suke; Su, Yanli; Zhang, Zhen; Qiao, Yushan; Li, Xiugen

2017-01-01

Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the 'Mantianhong' and 'Hongxiangsu' red-skinned cultivars. The 'Dangshansuli' cultivar genome was used as reference for sequence alignment. An average single-nucleotide polymorphism (SNP) index was calculated using a sliding window approach (200-kb windows, 20-kb increments). Nine scaffolds within the candidate QTL interval were in the fifth linkage group from 111.9 to 177.1 cM. There was a significant linkage between the insertions/deletions and simple sequence repeat markers designed from the candidate intervals and the red/green skin (R/G) locus, which was in a 582.5-kb candidate interval that contained 81 predicted protein-coding gene models and was composed of two subintervals at the bottom of the fifth chromosome. The ZFRI 130-16, In2130-12 and In2130-16 markers located near the R/G locus could potentially be used to identify the red skin trait in Asian pear populations. This study provides new insights into the genetics controlling the red skin phenotype in this fruit.

In search of Nemesis

NASA Technical Reports Server (NTRS)

Carlson, S.; Culler, T.; Muller, R. A.; Tetreault, M.; Perlmutter, S.

1994-01-01

The parallax of all stars of visual magnitude greater than about 6.5 has already been measured. If Nemesis is a main-sequence star 1 parsec away, this requires Nemesis's mass to be less than about 0.4 solar masses. If it were less than about 0.05 solar masses its gravity would be too weak to trigger a comet storm. If Nemesis is on the main sequence, this mass range requires it to be a red dwarf. A red dwarf companion would probably have been missed by standard astronomical surveys. Nearby stars are usually found because they are bright or have high proper motion. However, Nemesis's proper motion would now be 0.01 arcsec/yr, and if it is a red dwarf its magnitude is about 10 - too dim to attract attention. Unfortunately, standard four-color photometry does not distinguish between red dwarfs and giants. So although surveys such as the Dearborn Red Star Catalog list stars by magnitude and spectral type, they do not identify the dwarfs. Every star of the correct spectral type and magnitude must be scrutinized. Our candidate list is a hybrid; candidate red stars are identified in the astrometrically poor Dearborn Red Star Catalog and their positions are corrected using the Hubble Guide Star Catalog. When errors in the Dearborn catalog make it impossible to identify the corresponding Hubble star, the fields are split so that we have one centering on each possible candidate. We are currently scrutinizing 3098 fields, which we believe contain all possible red dwarf candidates in the northern hemisphere. Since our last report the analysis and database software has been completely rebuilt to take advantage of updated hardware, to make the data more accessible, and to implement improved methods of data analysis. The software is now completed and we are eliminating stars every clear night.

Identification of Multiple Novel Viruses, Including a Parvovirus and a Hepevirus, in Feces of Red Foxes

PubMed Central

van der Giessen, Joke; Haagmans, Bart L.; Osterhaus, Albert D. M. E.; Smits, Saskia L.

2013-01-01

Red foxes (Vulpes vulpes) are the most widespread members of the order of Carnivora. Since they often live in (peri)urban areas, they are a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. Here we evaluated the fecal viral microbiome of 13 red foxes by random PCR in combination with next-generation sequencing. Various novel viruses, including a parvovirus, bocavirus, adeno-associated virus, hepevirus, astroviruses, and picobirnaviruses, were identified. PMID:23616657

Characterization of Novel Simian Immunodeficiency Viruses from Red-Capped Mangabeys from Nigeria (SIVrcmNG409 and -NG411)

PubMed Central

Beer, Brigitte E.; Foley, Brian T.; Kuiken, Carla L.; Tooze, Zena; Goeken, Robert M.; Brown, Charles R.; Hu, Jinjie; Claire, Marisa St.; Korber, Bette T.; Hirsch, Vanessa M.

2001-01-01

Two novel simian immunodeficiency virus (SIV) strains from wild-caught red-capped mangabeys (Cercocebus torquatus torquatus) from Nigeria were characterized. Sequence analysis of the fully sequenced SIV strain rcmNG411 (SIVrcmNG411) and gag and pol sequence of SIVrcmNG409 revealed that they were genetically most closely related to the recently characterized SIVrcm from Gabon (SIVrcmGB1). Thus, red-capped mangabeys from distant geographic locations harbor a common lineage of SIV. SIVrcmNG411 carried a vpx gene in addition to vpr, suggesting a common evolutionary ancestor with SIVsm (from sooty mangabeys). However, SIVrcm was only marginally closer to SIVsm in that region than to any of the other lentiviruses. SIVrcm showed the highest similarity in pol with SIVdrl, isolated from a drill, a primate that is phylogenetically distinct from mangabey monkeys, and clustered with other primate lentiviruses (primarily SIVcpz [from chimpanzees] and SIVagmSab [from African green monkeys]) discordantly in different regions of the genome, suggesting a history of recombination. Despite the genetic relationship to SIVcpz in the pol gene, SIVrcmNG411 did not replicate in chimpanzee peripheral blood mononuclear cells (PBMC), although two other viruses unrelated to SIVcpz, SIVmndGB1 (from mandrills) and SIVlhoest (from L'Hoest monkeys), were able to grow in chimpanzee PBMC. The CCR5 24-bp deletion previously described in red-capped mangabeys from Gabon was also observed in Nigerian red-capped mangabeys, and SIVrcmNG411, like SIVrcmGB1, used CCR2B and STRL33 as coreceptors for virus entry. SIVrcm, SIVsm, SIVmndGB1, and all four SIVlhoest isolates but not SIVsun (from sun-tailed monkeys) replicated efficiently in human PBMC, suggesting that the ability to infect the human host can vary within one lineage. PMID:11711592

Sediment budget as affected by construction of a sequence of dams in the lower Red River, Viet Nam

NASA Astrophysics Data System (ADS)

Lu, Xi Xi; Oeurng, Chantha; Le, Thi Phuong Quynh; Thuy, Duong Thi

2015-11-01

Dam construction is one of the main factors resulting in riverine sediment changes, which in turn cause river degradation or aggradation downstream. The main objective of this work is to examine the sediment budget affected by a sequence of dams constructed upstream in the lower reach of the Red River. The study is based on the longer-term annual data (1960-2010) with a complementary daily water and sediment data set (2008-2010). The results showed that the stretch of the river changed from sediment surplus (suggesting possible deposition processes) into sediment deficit (possible erosion processes) after the first dam (Thac Ba Dam) was constructed in 1972 and changed back to deposition after the second dam (Hoa Binh Dam) was constructed in 1985. The annual sediment deposition varied between 1.9 Mt/y and 46.7 Mt/y with an annual mean value of 22.9 Mt/y (1985-2010). The sediment deposition at the lower reach of the Red River would accelerate river aggradation which would change river channel capacity in the downstream of the Red River. The depositional processes could be sustained or changed back to erosional processes after more dams (the amount of sediment deposit was much less after the latest two dams Tuyen Quang Dam in 2009 and Sonla Dam in 2010) are constructed, depending on the water and sediment dynamics. This study revealed that the erosional and depositional processes could be shifted for the same stretch of river as affected by a sequence of dams and provides useful insights in river management in order to reduce flood frequency along the lower reach of the Red River.

Light regulation of the abundance of mRNA encoding a nucleolin-like protein localized in the nucleoli of pea nuclei.

PubMed Central

Tong, C G; Reichler, S; Blumenthal, S; Balk, J; Hsieh, H L; Roux, S J

1997-01-01

A cDNA encoding a nucleolar protein was selected from a pea (Pisum sativum) plumule library, cloned, and sequenced. The translated sequence of the cDNA has significant percent identity to Xenopus laevis nucleolin (31%), the alfalfa (Medicago sativa) nucleolin homolog (66%), and the yeast (Saccharomyces cerevisiae) nucleolin homolog (NSR1) (28%). It also has sequence patterns in its primary structure that are characteristic of all nucleolins, including an N-terminal acidic motif, RNA recognition motifs, and a C-terminal Gly- and Arg-rich domain. By immunoblot analysis, the polyclonal antibodies used to select the cDNA bind selectively to a 90-kD protein in purified pea nuclei and nucleoli and to an 88-kD protein in extracts of Escherichia coli expressing the cDNA. In immunolocalization assays of pea plumule cells, the antibodies stained primarily a region surrounding the fibrillar center of nucleoli, where animal nucleolins are typically found. Southern analysis indicated that the pea nucleolin-like protein is encoded by a single gene, and northern analysis showed that the labeled cDNA binds to a single band of RNA, approximately the same size and the cDNA. After irradiation of etiolated pea seedlings by red light, the mRNA level in plumules decreased during the 1st hour and then increased to a peak of six times the 0-h level at 12 h. Far-red light reversed this effect of red light, and the mRNA accumulation from red/far-red light irradiation was equal to that found in the dark control. This indicates that phytochrome may regulate the expression of this gene. PMID:9193096

360 degree vision system: opportunities in transportation

NASA Astrophysics Data System (ADS)

Thibault, Simon

2007-09-01

Panoramic technologies are experiencing new and exciting opportunities in the transportation industries. The advantages of panoramic imagers are numerous: increased areas coverage with fewer cameras, imaging of multiple target simultaneously, instantaneous full horizon detection, easier integration of various applications on the same imager and others. This paper reports our work on panomorph optics and potential usage in transportation applications. The novel panomorph lens is a new type of high resolution panoramic imager perfectly suitable for the transportation industries. The panomorph lens uses optimization techniques to improve the performance of a customized optical system for specific applications. By adding a custom angle to pixel relation at the optical design stage, the optical system provides an ideal image coverage which is designed to reduce and optimize the processing. The optics can be customized for the visible, near infra-red (NIR) or infra-red (IR) wavebands. The panomorph lens is designed to optimize the cost per pixel which is particularly important in the IR. We discuss the use of the 360 vision system which can enhance on board collision avoidance systems, intelligent cruise controls and parking assistance. 360 panoramic vision systems might enable safer highways and significant reduction in casualties.

Stochastic environmental fluctuations drive epidemiology in experimental host–parasite metapopulations

PubMed Central

Duncan, Alison B.; Gonzalez, Andrew; Kaltz, Oliver

2013-01-01

Environmental fluctuations are important for parasite spread and persistence. However, the effects of the spatial and temporal structure of environmental fluctuations on host–parasite dynamics are not well understood. Temporal fluctuations can be random but positively autocorrelated, such that the environment is similar to the recent past (red noise), or random and uncorrelated with the past (white noise). We imposed red or white temporal temperature fluctuations on experimental metapopulations of Paramecium caudatum, experiencing an epidemic of the bacterial parasite Holospora undulata. Metapopulations (two subpopulations linked by migration) experienced fluctuations between stressful (5°C) and permissive (23°C) conditions following red or white temporal sequences. Spatial variation in temperature fluctuations was implemented by exposing subpopulations to the same (synchronous temperatures) or different (asynchronous temperatures) temporal sequences. Red noise, compared with white noise, enhanced parasite persistence. Despite this, red noise coupled with asynchronous temperatures allowed infected host populations to maintain sizes equivalent to uninfected populations. It is likely that this occurs because subpopulations in permissive conditions rescue declining subpopulations in stressful conditions. We show how patterns of temporal and spatial environmental fluctuations can impact parasite spread and host population abundance. We conclude that accurate prediction of parasite epidemics may require realistic models of environmental noise. PMID:23966645

The Red Spiral Galaxy UGC11680: Clues for the Inside-Out Quenching.

NASA Astrophysics Data System (ADS)

Bárcenas, J.; Sanchez, S. F.

2016-06-01

Broadly, galaxies can be divided in two groups, thanks to the Color-Magnitude Diagram: the lively star formation ones, ``The blue Cloud'' and galaxies which halted their star formation, ``The Red Sequence''. It is a currently accepted that the galaxies start their lifespan as a blue objects, turning red when they stop to assembly more mass and thus more stars. Nevertheless, This change need to be quick (˜ 1 Gyr), due to the dearth of galaxies between this two populations (the so called ``green valley'').Previous works have found two distinct stellar mass assembly modes, they are termed as ``the inside-out'' and ``the outside-in'' growth scenarios in the literature. In the ``inside-out'' scenario, mass assembly is finished in the galactic central region. In some cases, the inflow gas can fuel the central SuperMassive BlackHole. The subsequent AGN feedback will then shut-off the central star formation. One possible case of this scenario is the galaxy UGC11680, an unusual face-on red spiral galaxy with an AGN type 2, at the red sequence belonging to the CALIFA survey. We used the so called fossil method to study its star formation history and try to understand what happened to its stellar populations.

Outbreak and genotyping of canine distemper virus in captive Siberian tigers and red pandas.

PubMed

Zhang, He; Shan, Fen; Zhou, Xia; Li, Bing; Zhai, Jun-Qiong; Zou, Shu-Zhan; Wu, Meng-Fan; Chen, Wu; Zhai, Shao-Lun; Luo, Man-Lin

2017-08-15

In this study, four canine distemper virus (CDV) strains were isolated from captive Siberian tigers (Panthera tigris altaica) and red pandas (Ailurus fulgens) during two separate CDV outbreaks in a zoo in Guangdong province, China. Sequence alignment and phylogenetic analyses based on the full-length hemagglutinin (H) and fusion (F) genes showed that they were closely identical to genotype Asia-1. Prior to confirmation of CDV in Siberian tigers, to control spread of the disease, a live attenuated combination CDV vaccine was used among almost all carnivore animals except for red pandas in which another recombinant combination CDV vaccine was used. However, about two months later, CDV re-emerged and caused the death among red pandas. Based on the vaccination records, the live combination vaccine could be considered an ideal weapon against CDV in zoo carnivore animals. Although the recombinant combination CDV vaccine was safe for red pandas, its protection effectiveness remains to be further investigated. Moreover, according to the outbreak interval time and sequence characterization, we suspected that stray cats circulating in the zoo were the intermediate host, which contributed to CDV spread from stray dogs to zoo animals. This study revealed the importance of vaccination and biosecurity for zoo animals.

[Correlation between adenylosuccinate lyase (ADSL) gene polymorphism and inosine monophosphate acid (IMP) content in domestic fowl and genetic relationship between red jungle fowl and domestic fowl].

PubMed

Shu, Jing-Ting; Bao, Wen-Bin; Zhang, Hong-Xia; Zhang, Xue-Yu; Ji, Cong-Liang; Chen, Guo-Hong

2007-03-01

This study investigates single nucleotide polymorphism (SNP) of the adenylosuccinate lyase(ADSL) gene in variety chicken breeds, including Recessive White chickens, Silkies chickens, Baier chickens, Tibetan chickens and two red jungle fowls. Primers for exon 2 in ADSL gene were designed based on the chicken genomic sequence and a SNP(C/T at 3484) was detected by PCR-SSCP and DNA sequencing. Three genotypes within all breeds were found and least square analysis showed that TT genotype birds had a significant higher inosine monophosphate acid (IMP) content than TC (P < 0.01) and CC (P < 0.05) genotype birds, TC genotype birds had a little higher IMP content than CC genotype birds, but the difference was not significant. We proposed this SNP site correlated with IMP content in chickens. A neighbour-joining dendrogram was constructed based on the Nei's genentic distance. The genetic relationship between Chinese red jungle fowl and Tibetan chickens was the nearest, whereas Baier chickens were more closer to Silkies chickens. The Chinese red jungle fowls were relatively closer to the domestic fowls, whereas Thailand red jungle fowls were relatively diverging to the Chinese native breeds. These results supported the theory concerning the independent origins of Chinese native fowl breeds.

The genome of the diatom Thalassiosira pseudonana: Ecology,evolution, and metabolism

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

Ambrust, E.V.; Berges, J.; Bowler, C.

2004-09-01

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for {approx}20% of global carbon fixation. We report the 34 Mbp draft nuclear genome of the marine diatom, Thalassiosira pseudonana and its 129 Kbp plastid and 44 Kbp mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, utilization of a range of nitrogenous compounds and a complete urea cycle, all attributes that allow diatoms to prosper in themore » marine environment. Diatoms are unicellular, photosynthetic, eukaryotic algae found throughout the world's oceans and freshwater systems. They form the base of short, energetically-efficient food webs that support large-scale coastal fisheries. Photosynthesis by marine diatoms generates as much as 40% of the 45-50 billion tonnes of organic carbon produced each year in the sea (1), and their role in global carbon cycling is predicted to be comparable to that of all terrestrial rainforests combined (2, 3). Over geological time, diatoms may have influenced global climate by changing the flux of atmospheric carbon dioxide into the oceans (4). A defining feature of diatoms is their ornately patterned silicified cell wall or frustule, which displays species-specific nano-structures of such fine detail that diatoms have long been used to test the resolution of optical microscopes. Recent attention has focused on biosynthesis of these nano-structures as a paradigm for future silica nanotechnology (5). The long history (over 180 million years) and dominance of diatoms in the oceans is reflected by their contributions to vast deposits of diatomite, most cherts and a significant fraction of current petroleum reserves (6). As photosynthetic heterokonts, diatoms reflect a fundamentally different evolutionary history from the higher plants that dominate photosynthesis on land. Higher plants and green, red and glaucophyte algae are derived from a primary endosymbiotic event in which a non-photosynthetic eukaryote acquired a chloroplast by engulfing (or being invaded by) a prokaryotic cyanobacterium. In contrast, dominant bloom-forming eukaryotic phytoplankton in the ocean, such as diatoms and haptophytes, were derived by secondary endosymbiosis whereby a non-photosynthetic eukaryote acquired a chloroplast by engulfing a photosynthetic eukaryote, probably a red algal endosymbiont (Fig. 1). Each endosymbiotic event led to new combinations of genes derived from the hosts and endosymbionts (7). Prior to this project, relatively few diatom genes had been sequenced, few chromosome numbers were known, and genetic maps did not exist (8). The ecological and evolutionary importance of diatoms motivated our sequencing and analysis of the nuclear, plastid, and mitochondrial genomes of the marine centric diatom Thalassiosira pseudonana.« less

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

Armbrust, E V; Berges, J A; Bowler, C

Diatoms are unicellular algae with plastids acquired by secondary endosymbiosis. They are responsible for {approx}20% of global carbon fixation. We report the 34 Mbp draft nuclear genome of the marine diatom, Thalassiosira pseudonana and its 129 Kbp plastid and 44 Kbp mitochondrial genomes. Sequence and optical restriction mapping revealed 24 diploid nuclear chromosomes. We identified novel genes for silicic acid transport and formation of silica-based cell walls, high-affinity iron uptake, biosynthetic enzymes for several types of polyunsaturated fatty acids, utilization of a range of nitrogenous compounds and a complete urea cycle, all attributes that allow diatoms to prosper in themore » marine environment. Diatoms are unicellular, photosynthetic, eukaryotic algae found throughout the world's oceans and freshwater systems. They form the base of short, energetically-efficient food webs that support large-scale coastal fisheries. Photosynthesis by marine diatoms generates as much as 40% of the 45-50 billion tonnes of organic carbon produced each year in the sea (1), and their role in global carbon cycling is predicted to be comparable to that of all terrestrial rainforests combined (2, 3). Over geological time, diatoms may have influenced global climate by changing the flux of atmospheric carbon dioxide into the oceans (4). A defining feature of diatoms is their ornately patterned silicified cell wall or frustule, which displays species-specific nano-structures of such fine detail that diatoms have long been used to test the resolution of optical microscopes. Recent attention has focused on biosynthesis of these nano-structures as a paradigm for future silica nanotechnology (5). The long history (over 180 million years) and dominance of diatoms in the oceans is reflected by their contributions to vast deposits of diatomite, most cherts and a significant fraction of current petroleum reserves (6). As photosynthetic heterokonts, diatoms reflect a fundamentally different evolutionary history from the higher plants that dominate photosynthesis on land. Higher plants and green, red and glaucophyte algae are derived from a primary endosymbiotic event in which a non-photosynthetic eukaryote acquired a chloroplast by engulfing (or being invaded by) a prokaryotic cyanobacterium. In contrast, dominant bloom-forming eukaryotic phytoplankton in the ocean, such as diatoms and haptophytes, were derived by secondary endosymbiosis whereby a non-photosynthetic eukaryote acquired a chloroplast by engulfing a photosynthetic eukaryote, probably a red algal endosymbiont (Fig. 1). Each endosymbiotic event led to new combinations of genes derived from the hosts and endosymbionts (7). Prior to this project, relatively few diatom genes had been sequenced, few chromosome numbers were known, and genetic maps did not exist (8). The ecological and evolutionary importance of diatoms motivated our sequencing and analysis of the nuclear, plastid, and mitochondrial genomes of the marine centric diatom Thalassiosira pseudonana.« less

Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential.

PubMed

Al-Amoudi, Soha; Essack, Magbubah; Simões, Marta F; Bougouffa, Salim; Soloviev, Irina; Archer, John A C; Lafi, Feras F; Bajic, Vladimir B

2016-09-10

Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds.

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

PubMed

Pilkington, Sarah M; Crowhurst, Ross; Hilario, Elena; Nardozza, Simona; Fraser, Lena; Peng, Yongyan; Gunaseelan, Kularajathevan; Simpson, Robert; Tahir, Jibran; Deroles, Simon C; Templeton, Kerry; Luo, Zhiwei; Davy, Marcus; Cheng, Canhong; McNeilage, Mark; Scaglione, Davide; Liu, Yifei; Zhang, Qiong; Datson, Paul; De Silva, Nihal; Gardiner, Susan E; Bassett, Heather; Chagné, David; McCallum, John; Dzierzon, Helge; Deng, Cecilia; Wang, Yen-Yi; Barron, Lorna; Manako, Kelvina; Bowen, Judith; Foster, Toshi M; Erridge, Zoe A; Tiffin, Heather; Waite, Chethi N; Davies, Kevin M; Grierson, Ella P; Laing, William A; Kirk, Rebecca; Chen, Xiuyin; Wood, Marion; Montefiori, Mirco; Brummell, David A; Schwinn, Kathy E; Catanach, Andrew; Fullerton, Christina; Li, Dawei; Meiyalaghan, Sathiyamoorthy; Nieuwenhuizen, Niels; Read, Nicola; Prakash, Roneel; Hunter, Don; Zhang, Huaibi; McKenzie, Marian; Knäbel, Mareike; Harris, Alastair; Allan, Andrew C; Gleave, Andrew; Chen, Angela; Janssen, Bart J; Plunkett, Blue; Ampomah-Dwamena, Charles; Voogd, Charlotte; Leif, Davin; Lafferty, Declan; Souleyre, Edwige J F; Varkonyi-Gasic, Erika; Gambi, Francesco; Hanley, Jenny; Yao, Jia-Long; Cheung, Joey; David, Karine M; Warren, Ben; Marsh, Ken; Snowden, Kimberley C; Lin-Wang, Kui; Brian, Lara; Martinez-Sanchez, Marcela; Wang, Mindy; Ileperuma, Nadeesha; Macnee, Nikolai; Campin, Robert; McAtee, Peter; Drummond, Revel S M; Espley, Richard V; Ireland, Hilary S; Wu, Rongmei; Atkinson, Ross G; Karunairetnam, Sakuntala; Bulley, Sean; Chunkath, Shayhan; Hanley, Zac; Storey, Roy; Thrimawithana, Amali H; Thomson, Susan; David, Charles; Testolin, Raffaele; Huang, Hongwen; Hellens, Roger P; Schaffer, Robert J

2018-04-16

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

Eukaryotic algal phytochromes span the visible spectrum

PubMed Central

Rockwell, Nathan C.; Duanmu, Deqiang; Martin, Shelley S.; Bachy, Charles; Price, Dana C.; Bhattacharya, Debashish; Worden, Alexandra Z.; Lagarias, J. Clark

2014-01-01

Plant phytochromes are photoswitchable red/far-red photoreceptors that allow competition with neighboring plants for photosynthetically active red light. In aquatic environments, red and far-red light are rapidly attenuated with depth; therefore, photosynthetic species must use shorter wavelengths of light. Nevertheless, phytochrome-related proteins are found in recently sequenced genomes of many eukaryotic algae from aquatic environments. We examined the photosensory properties of seven phytochromes from diverse algae: four prasinophyte (green algal) species, the heterokont (brown algal) Ectocarpus siliculosus, and two glaucophyte species. We demonstrate that algal phytochromes are not limited to red and far-red responses. Instead, different algal phytochromes can sense orange, green, and even blue light. Characterization of these previously undescribed photosensors using CD spectroscopy supports a structurally heterogeneous chromophore in the far-red–absorbing photostate. Our study thus demonstrates that extensive spectral tuning of phytochromes has evolved in phylogenetically distinct lineages of aquatic photosynthetic eukaryotes. PMID:24567382

Automatic tracking of red blood cells in micro channels using OpenCV

NASA Astrophysics Data System (ADS)

Rodrigues, Vânia; Rodrigues, Pedro J.; Pereira, Ana I.; Lima, Rui

2013-10-01

The present study aims to developan automatic method able to track red blood cells (RBCs) trajectories flowing through a microchannel using the Open Source Computer Vision (OpenCV). The developed method is based on optical flux calculation assisted by the maximization of the template-matching product. The experimental results show a good functional performance of this method.

Optical ridge waveguides in Er3+/Yb3+ co-doped phosphate glass produced by ion irradiation combined with femtosecond laser ablation for guided-wave green and red upconversion emissions

NASA Astrophysics Data System (ADS)

Chen, Chen; He, Ruiyun; Tan, Yang; Wang, Biao; Akhmadaliev, Shavkat; Zhou, Shengqiang; de Aldana, Javier R. Vázquez; Hu, Lili; Chen, Feng

2016-01-01

This work reports on the fabrication of ridge waveguides in Er3+/Yb3+ co-doped phosphate glass by the combination of femtosecond laser ablation and following swift carbon ion irradiation. The guiding properties of waveguides have been investigated at 633 and 1064 nm through end face coupling arrangement. The refractive index profile on the cross section of the waveguide has been constructed. The propagation losses can be reduced considerably after annealing treatment. Under the optical pump laser at 980 nm, the upconversion emission of both green and red fluorescence has been realized through the ridge waveguide structures.

Use of a night vision intensifier for direct visualization by eye of far-red and near-infrared fluorescence through an optical microscope.

PubMed

Siddiqi, M A; Kilduff, G M; Gearhart, J D

2003-11-01

We describe the design, construction and testing of a prototype device that allows the direct visualization by eye of far-red and near-infrared (NIR) fluorescence through an optical microscope. The device incorporates a gallium arsenide (GaAs) image intensifier, typically utilized in low-light or 'night vision' applications. The intensifier converts far-red and NIR light into electrons and then into green light, which is visible to the human eye. The prototype makes possible the direct, real-time viewing by eye of normally invisible far-red and NIR fluorescence from a wide variety of fluorophores, using the full field of view of the microscope to which it is applied. The high sensitivity of the image intensifier facilitates the viewing of a wide variety of photosensitive specimens, including live cells and embryos, at vastly reduced illumination levels in both fluorescence and bright-field microscopy. Modifications to the microscope are not required in order to use the prototype, which is fully compatible with all current fluorescence techniques. Refined versions of the prototype device will have broad research and clinical applications.

Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy.

PubMed

Levy-Sakin, Michal; Ebenstein, Yuval

2013-08-01

Next generation sequencing (NGS) is revolutionizing all fields of biological research but it fails to extract the full range of information associated with genetic material. Optical mapping of DNA grants access to genetic and epigenetic information on individual DNA molecules up to ∼1 Mbp in length. Fluorescent labeling of specific sequence motifs, epigenetic marks and other genomic information on individual DNA molecules generates a high content optical barcode along the DNA. By stretching the DNA to a linear configuration this barcode may be directly visualized by fluorescence microscopy. We discuss the advances of these methods in light of recent developments in nano-fabrication and super-resolution optical imaging (nanoscopy) and review the latest achievements of optical mapping in the context of genomic analysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

A novel all-optical label processing based on multiple optical orthogonal codes sequences for optical packet switching networks

NASA Astrophysics Data System (ADS)

Zhang, Chongfu; Qiu, Kun; Xu, Bo; Ling, Yun

2008-05-01

This paper proposes an all-optical label processing scheme that uses the multiple optical orthogonal codes sequences (MOOCS)-based optical label for optical packet switching (OPS) (MOOCS-OPS) networks. In this scheme, each MOOCS is a permutation or combination of the multiple optical orthogonal codes (MOOC) selected from the multiple-groups optical orthogonal codes (MGOOC). Following a comparison of different optical label processing (OLP) schemes, the principles of MOOCS-OPS network are given and analyzed. Firstly, theoretical analyses are used to prove that MOOCS is able to greatly enlarge the number of available optical labels when compared to the previous single optical orthogonal code (SOOC) for OPS (SOOC-OPS) network. Then, the key units of the MOOCS-based optical label packets, including optical packet generation, optical label erasing, optical label extraction and optical label rewriting etc., are given and studied. These results are used to verify that the proposed MOOCS-OPS scheme is feasible.

M dwarf spectra from 0.6 to 1.5 micron - A spectral sequence, model atmosphere fitting, and the temperature scale

NASA Technical Reports Server (NTRS)

Kirkpatrick, J. D.; Kelly, Douglas M.; Rieke, George H.; Liebert, James; Allard, France; Wehrse, Rainer

1993-01-01

Red/infrared (0.6-1.5 micron) spectra are presented for a sequence of well-studied M dwarfs ranging from M2 through M9. A variety of temperature-sensitive features useful for spectral classification are identified. Using these features, the spectral data are compared to recent theoretical models, from which a temperature scale is assigned. The red portion of the model spectra provide reasonably good fits for dwarfs earlier than M6. For layer types, the infrared region provides a more reliable fit to the observations. In each case, the wavelength region used includes the broad peak of the energy distribution. For a given spectral type, the derived temperature sequence assigns higher temperatures than have earlier studies - the difference becoming more pronounced at lower luminosities. The positions of M dwarfs on the H-R diagram are, as a result, in closer agreement with theoretical tracks of the lower main sequence.

The Electromagnetic Counterpart of the Binary Neutron Star Merger LIGO/Virgo GW170817. II. UV, Optical, and Near-infrared Light Curves and Comparison to Kilonova Models

NASA Astrophysics Data System (ADS)

Cowperthwaite, P. S.; Berger, E.; Villar, V. A.; Metzger, B. D.; Nicholl, M.; Chornock, R.; Blanchard, P. K.; Fong, W.; Margutti, R.; Soares-Santos, M.; Alexander, K. D.; Allam, S.; Annis, J.; Brout, D.; Brown, D. A.; Butler, R. E.; Chen, H.-Y.; Diehl, H. T.; Doctor, Z.; Drout, M. R.; Eftekhari, T.; Farr, B.; Finley, D. A.; Foley, R. J.; Frieman, J. A.; Fryer, C. L.; García-Bellido, J.; Gill, M. S. S.; Guillochon, J.; Herner, K.; Holz, D. E.; Kasen, D.; Kessler, R.; Marriner, J.; Matheson, T.; Neilsen, E. H., Jr.; Quataert, E.; Palmese, A.; Rest, A.; Sako, M.; Scolnic, D. M.; Smith, N.; Tucker, D. L.; Williams, P. K. G.; Balbinot, E.; Carlin, J. L.; Cook, E. R.; Durret, F.; Li, T. S.; Lopes, P. A. A.; Lourenço, A. C. C.; Marshall, J. L.; Medina, G. E.; Muir, J.; Muñoz, R. R.; Sauseda, M.; Schlegel, D. J.; Secco, L. F.; Vivas, A. K.; Wester, W.; Zenteno, A.; Zhang, Y.; Abbott, T. M. C.; Banerji, M.; Bechtol, K.; Benoit-Lévy, A.; Bertin, E.; Buckley-Geer, E.; Burke, D. L.; Capozzi, D.; Carnero Rosell, A.; Carrasco Kind, M.; Castander, F. J.; Crocce, M.; Cunha, C. E.; D'Andrea, C. B.; da Costa, L. N.; Davis, C.; DePoy, D. L.; Desai, S.; Dietrich, J. P.; Drlica-Wagner, A.; Eifler, T. F.; Evrard, A. E.; Fernandez, E.; Flaugher, B.; Fosalba, P.; Gaztanaga, E.; Gerdes, D. W.; Giannantonio, T.; Goldstein, D. A.; Gruen, D.; Gruendl, R. A.; Gutierrez, G.; Honscheid, K.; Jain, B.; James, D. J.; Jeltema, T.; Johnson, M. W. G.; Johnson, M. D.; Kent, S.; Krause, E.; Kron, R.; Kuehn, K.; Nuropatkin, N.; Lahav, O.; Lima, M.; Lin, H.; Maia, M. A. G.; March, M.; Martini, P.; McMahon, R. G.; Menanteau, F.; Miller, C. J.; Miquel, R.; Mohr, J. J.; Neilsen, E.; Nichol, R. C.; Ogando, R. L. C.; Plazas, A. A.; Roe, N.; Romer, A. K.; Roodman, A.; Rykoff, E. S.; Sanchez, E.; Scarpine, V.; Schindler, R.; Schubnell, M.; Sevilla-Noarbe, I.; Smith, M.; Smith, R. C.; Sobreira, F.; Suchyta, E.; Swanson, M. E. C.; Tarle, G.; Thomas, D.; Thomas, R. C.; Troxel, M. A.; Vikram, V.; Walker, A. R.; Wechsler, R. H.; Weller, J.; Yanny, B.; Zuntz, J.

2017-10-01

We present UV, optical, and near-infrared (NIR) photometry of the first electromagnetic counterpart to a gravitational wave source from Advanced Laser Interferometer Gravitational-wave Observatory (LIGO)/Virgo, the binary neutron star merger GW170817. Our data set extends from the discovery of the optical counterpart at 0.47-18.5 days post-merger, and includes observations with the Dark Energy Camera (DECam), Gemini-South/FLAMINGOS-2 (GS/F2), and the Hubble Space Telescope (HST). The spectral energy distribution (SED) inferred from this photometry at 0.6 days is well described by a blackbody model with T≈ 8300 K, a radius of R≈ 4.5× {10}14 cm (corresponding to an expansion velocity of v≈ 0.3c), and a bolometric luminosity of {L}{bol}≈ 5× {10}41 erg s-1. At 1.5 days we find a multi-component SED across the optical and NIR, and subsequently we observe rapid fading in the UV and blue optical bands and significant reddening of the optical/NIR colors. Modeling the entire data set, we find that models with heating from radioactive decay of 56Ni, or those with only a single component of opacity from r-process elements, fail to capture the rapid optical decline and red optical/NIR colors. Instead, models with two components consistent with lanthanide-poor and lanthanide-rich ejecta provide a good fit to the data; the resulting “blue” component has {M}{ej}{blue}≈ 0.01 {M}⊙ and {v}{ej}{blue}≈ 0.3 {{c}}, and the “red” component has {M}{ej}{red}≈ 0.04 {M}⊙ and {v}{ej}{red}≈ 0.1 {{c}}. These ejecta masses are broadly consistent with the estimated r-process production rate required to explain the Milky Way r-process abundances, providing the first evidence that binary neutron star (BNS) mergers can be a dominant site of r-process enrichment.

Characterization of short interspersed elements (SINEs) in a red alga, Porphyra yezoensis.

PubMed

Zhang, Wenbo; Lin, Xiaofei; Peddigari, Suresh; Takechi, Katsuaki; Takano, Hiroyoshi; Takio, Susumu

2007-02-01

Short interspersed element (SINE)-like sequences referred to as PySN1 and PySN2 were identified in a red alga, Porphyra yezoensis. Both elements contained an internal promoter with motifs (A box and B box) recognized by RNA polymerase III, and target site duplications at both ends. Genomic Southern blot analysis revealed that both elements were widely and abundantly distributed on the genome. 3' and 5' RACE suggested that PySN1 was expressed as a chimera transcript with flanking SINE-unrelated sequences and possessed the poly-A tail at the same position near the 3' end of PySN1.

SN 1987A - The evolution from red to blue

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

Tuchman, Y.; Wheeler, J.C.

1989-11-01

Envelope models in thermal and dynamic equilibrium are used to explore the nature of the transition of SK -69 deg 202, the progenitor of SN 1987A, from the Hayashi track to its final blue position in the H-R diagram. Loci of possible thermal equilibrium solutions are presented as a function of Teff and M(C/O), the mass of the carbon/oxygen core interior to the helium burning shell. It is found that uniform helium enrichment of the envelope results in red-blue evolution but that the resulting blue solution is much hotter than SK -69 deg 202. Solutions in which the only changemore » is to redistribute the portion of the envelope enriched in helium during main-sequence convective core contraction into a step function with Y of about 0.5 at a mass cut of about 10 solar masses give a natural transition from red to blue and a final value of Teff in agreement with observations. It is argued that SK -69 deg 202 probably fell on a post-Hayashi track sequence at moderate Teff. The possible connection of this sequence to the step distribution in the H-R diagram of the LMC. 19 refs.« less

QUENCHING STAR FORMATION AT INTERMEDIATE REDSHIFTS: DOWNSIZING OF THE MASS FLUX DENSITY IN THE GREEN VALLEY

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

Goncalves, Thiago S.; Menendez-Delmestre, Karin; Martin, D. Christopher

2012-11-01

The bimodality in galaxy properties has been observed at low and high redshifts, with a clear distinction between star-forming galaxies in the blue cloud and passively evolving objects in the red sequence; the absence of galaxies with intermediate properties indicates that the quenching of star formation and subsequent transition between populations must happen rapidly. In this paper, we present a study of over 100 transiting galaxies in the so-called green valley at intermediate redshifts (z {approx} 0.8). By using very deep spectroscopy with the DEIMOS instrument at the Keck telescope we are able to infer the star formation histories ofmore » these objects and measure the stellar mass flux density transiting from the blue cloud to the red sequence when the universe was half its current age. Our results indicate that the process happened more rapidly and for more massive galaxies in the past, suggesting a top-down scenario in which the massive end of the red sequence is forming first. This represents another aspect of downsizing, with the mass flux density moving toward smaller galaxies in recent times.« less

RADIO EMISSION FROM RED-GIANT HOT JUPITERS

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

Fujii, Yuka; Spiegel, David S.; Mroczkowski, Tony

2016-04-01

When planet-hosting stars evolve off the main sequence and go through the red-giant branch, the stars become orders of magnitudes more luminous and, at the same time, lose mass at much higher rates than their main-sequence counterparts. Accordingly, if planetary companions exist around these stars at orbital distances of a few au, they will be heated up to the level of canonical hot Jupiters and also be subjected to a dense stellar wind. Given that magnetized planets interacting with stellar winds emit radio waves, such “Red-Giant Hot Jupiters” (RGHJs) may also be candidate radio emitters. We estimate the spectral auroralmore » radio intensity of RGHJs based on the empirical relation with the stellar wind as well as a proposed scaling for planetary magnetic fields. RGHJs might be intrinsically as bright as or brighter than canonical hot Jupiters and about 100 times brighter than equivalent objects around main-sequence stars. We examine the capabilities of low-frequency radio observatories to detect this emission and find that the signal from an RGHJ may be detectable at distances up to a few hundred parsecs with the Square Kilometer Array.« less

Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria.

PubMed

Speth, Daan R; Lagkouvardos, Ilias; Wang, Yong; Qian, Pei-Yuan; Dutilh, Bas E; Jetten, Mike S M

2017-07-01

Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.

Variations in 5S rDNAs in diploid and tetraploid offspring of red crucian carp × common carp.

PubMed

Ye, Lihai; Zhang, Chun; Tang, Xiaojun; Chen, Yiyi; Liu, Shaojun

2017-08-08

The allotetraploid hybrid fish (4nAT) that was created in a previous study through an intergeneric cross between red crucian carp (Carassius auratus red var., ♀) and common carp (Cyprinus carpio L., ♂) provided an excellent platform to investigate the effect of hybridization and polyploidization on the evolution of 5S rDNA. The 5S rDNAs of paternal common carp were made up of a coding sequence (CDS) and a non-transcribed spacer (NTS) unit, and while the 5S rDNAs of maternal red crucian carp contained a CDS and a NTS unit, they also contained a variable number of interposed regions (IPRs). The CDSs of the 5S rDNAs in both parental fishes were conserved, while their NTS units seemed to have been subjected to rapid evolution. The diploid hybrid 2nF 1 inherited all the types of 5S rDNAs in both progenitors and there were no signs of homeologous recombination in the 5S rDNAs of 2nF 1 by sequencing of PCR products. We obtained two segments of 5S rDNA with a total length of 16,457 bp from allotetraploid offspring 4nAT through bacterial artificial chromosome (BAC) sequencing. Using this sequence together with the 5S rDNA sequences amplified from the genomic DNA of 4nAT, we deduced that the 5S rDNAs of 4nAT might be inherited from the maternal progenitor red crucian carp. Additionally, the IPRs in the 5S rDNAs of 4nAT contained A-repeats and TA-repeats, which was not the case for the IPRs in the 5S rDNAs of 2nF 1 . We also detected two signals of a 200-bp fragment of 5S rDNA in the chromosomes of parental progenitors and hybrid progenies by fluorescence in situ hybridization (FISH). We deduced that during the evolution of 5S rDNAs in different ploidy hybrid fishes, interlocus gene conversion events and tandem repeat insertion events might occurred in the process of polyploidization. This study provided new insights into the relationship among the evolution of 5S rDNAs, hybridization and polyploidization, which were significant in clarifying the genome evolution of polyploid fish.

The Optical/Near-infrared Extinction Law in Highly Reddened Regions

NASA Astrophysics Data System (ADS)

Hosek, Matthew W., Jr.; Lu, Jessica R.; Anderson, Jay; Do, Tuan; Schlafly, Edward F.; Ghez, Andrea M.; Clarkson, William I.; Morris, Mark R.; Albers, Saundra M.

2018-03-01

A precise extinction law is a critical input when interpreting observations of highly reddened sources such as young star clusters and the Galactic Center (GC). We use Hubble Space Telescope observations of a region of moderate extinction and a region of high extinction to measure the optical and near-infrared extinction law (0.8–2.2 μm). The moderate-extinction region is the young massive cluster Westerlund 1 (Wd1; A Ks ∼ 0.6 mag), where 453 proper-motion selected main-sequence stars are used to measure the shape of the extinction law. To quantify the shape, we define the parameter {{ \\mathcal S }}1/λ , which behaves similarly to a color-excess ratio, but is continuous as a function of wavelength. The high-extinction region is the GC (A Ks ∼ 2.5 mag), where 819 red clump stars are used to determine the normalization of the law. The best-fit extinction law is able to reproduce the Wd1 main-sequence colors, which previous laws misestimate by 10%–30%. The law is inconsistent with a single power law, even when only the near-infrared filters are considered, and has A F125W/A Ks and A F814W/A Ks values that are 18% and 24% higher than the commonly used Nishiyama et al. law, respectively. Using this law, we recalculate the Wd1 distance to be 3905 ± 422 pc from published observations of the eclipsing binary W13. This new extinction law should be used for highly reddened populations in the Milky Way, such as the Quintuplet cluster and Young Nuclear Cluster. A python code is provided to generate the law for future use.

Fast optical and X-ray variability in the UCXB 4U0614+09

NASA Astrophysics Data System (ADS)

Hakala, P. J.; Charles, P. A.; Muhli, P.

2011-09-01

We present results from several years of fast optical photometry of 4U0614+091 (V1055 Orionis), a candidate ultracompact X-ray binary most likely consisting of a neutron star and a degenerate secondary. We find evidence for strong accretion-driven variability at all epochs, which manifests itself as red noise. This flickering produces transient peaks in the observed power spectrum in the 15-65 min period range. Only in one of our 12 optical data sets can we see evidence for a period that cannot be reproduced using the red noise model. This period of 51 min coincides with the strongest period detected by Shahbaz et al. and can thus be taken as the prime candidate for the orbital period of the system. Furthermore, we find some tentative evidence for the X-ray versus optical flux anticorrelation discovered by Machin et al. using our data together with the all-sky X-ray monitoring data from RXTE/All Sky Monitor. We propose that the complex time series behaviour of 4U0614+09 is a result of drastic changes in the accretion disc geometry/structure on time-scales from hours to days. Finally, we want to draw attention to the interpretation of moderately strong peaks in the power spectra of especially accreting sources. Many of such 'periods' can probably be attributed to the presence of red noise (i.e. correlated events) in the data. Based on observations made with the Nordic Optical Telescope, operated on the island of La Palma jointly by Denmark, Finland, Iceland, Norway and Sweden, in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. Uses results provided by the ASM/RXTE teams at MIT and at the RXTE SOF and GOF at NASA's GSFC.

Accurate Spectral Fits of Jupiter's Great Red Spot: VIMS Visual Spectra Modelled with Chromophores Created by Photolyzed Ammonia Reacting with Acetyleneχ±

NASA Astrophysics Data System (ADS)

Baines, Kevin; Sromovsky, Lawrence A.; Fry, Patrick M.; Carlson, Robert W.; Momary, Thomas W.

2016-10-01

We report results incorporating the red-tinted photochemically-generated aerosols of Carlson et al (2016, Icarus 274, 106-115) in spectral models of Jupiter's Great Red Spot (GRS). Spectral models of the 0.35-1.0-micron spectrum show good agreement with Cassini/VIMS near-center-meridian and near-limb GRS spectra for model morphologies incorporating an optically-thin layer of Carlson (2016) aerosols at high altitudes, either at the top of the tropospheric GRS cloud, or in a distinct stratospheric haze layer. Specifically, a two-layer "crème brûlée" structure of the Mie-scattering Carlson et al (2016) chromophore attached to the top of a conservatively scattering (hereafter, "white") optically-thick cloud fits the spectra well. Currently, best agreement (reduced χ2 of 0.89 for the central-meridian spectrum) is found for a 0.195-0.217-bar, 0.19 ± 0.02 opacity layer of chromophores with mean particle radius of 0.14 ± 0.01 micron. As well, a structure with a detached stratospheric chromophore layer ~0.25 bar above a white tropospheric GRS cloud provides a good spectral match (reduced χ2 of 1.16). Alternatively, a cloud morphology with the chromophore coating white particles in a single optically- and physically-thick cloud (the "coated-shell model", initially explored by Carlson et al 2016) was found to give significantly inferior fits (best reduced χ2 of 2.9). Overall, we find that models accurately fit the GRS spectrum if (1) most of the optical depth of the chromophore is in a layer near the top of the main cloud or in a distinct separated layer above it, but is not uniformly distributed within the main cloud, (2) the chromophore consists of relatively small, 0.1-0.2-micron-radius particles, and (3) the chromophore layer optical depth is small, ~ 0.1-0.2. Thus, our analysis supports the exogenic origin of the red chromophore consistent with the Carlson et al (2016) photolytic production mechanism rather than an endogenic origin, such as upwelling of material from the depths of Jupiter.

Optimization of flow cytometric detection and cell sorting of transgenic Plasmodium parasites using interchangeable optical filters

PubMed Central

2012-01-01

Background Malaria remains a major cause of morbidity and mortality worldwide. Flow cytometry-based assays that take advantage of fluorescent protein (FP)-expressing malaria parasites have proven to be valuable tools for quantification and sorting of specific subpopulations of parasite-infected red blood cells. However, identification of rare subpopulations of parasites using green fluorescent protein (GFP) labelling is complicated by autofluorescence (AF) of red blood cells and low signal from transgenic parasites. It has been suggested that cell sorting yield could be improved by using filters that precisely match the emission spectrum of GFP. Methods Detection of transgenic Plasmodium falciparum parasites expressing either tdTomato or GFP was performed using a flow cytometer with interchangeable optical filters. Parasitaemia was evaluated using different optical filters and, after optimization of optics, the GFP-expressing parasites were sorted and analysed by microscopy after cytospin preparation and by imaging cytometry. Results A new approach to evaluate filter performance in flow cytometry using two-dimensional dot blot was developed. By selecting optical filters with narrow bandpass (BP) and maximum position of filter emission close to GFP maximum emission in the FL1 channel (510/20, 512/20 and 517/20; dichroics 502LP and 466LP), AF was markedly decreased and signal-background improve dramatically. Sorting of GFP-expressing parasite populations in infected red blood cells at 90 or 95% purity with these filters resulted in 50-150% increased yield when compared to the standard filter set-up. The purity of the sorted population was confirmed using imaging cytometry and microscopy of cytospin preparations of sorted red blood cells infected with transgenic malaria parasites. Discussion Filter optimization is particularly important for applications where the FP signal and percentage of positive events are relatively low, such as analysis of parasite-infected samples with in the intention of gene-expression profiling and analysis. The approach outlined here results in substantially improved yield of GFP-expressing parasites, and requires decreased sorting time in comparison to standard methods. It is anticipated that this protocol will be useful for a wide range of applications involving rare events. PMID:22950515

Foliar Reflectance and Fluorescence Responses for Corn and Soybean Plants Under Nitrogen Stress

NASA Technical Reports Server (NTRS)

Middleton, E. M.; Campbell, P. K. Entcheva; Corp, L. A.; Butcher, L. M.; McMurtrey, J. E.

2003-01-01

We are investigating the use of spectral indices derived from actively induced fluorescence spectra and passive optical spectra. We examined the influence of photosynthetic pigment, carbon (C) and nitrogen (N) content on the spectral fluorescence and passive optical property characteristics of mature, upper leaves from plants provided different N fertilizer application rates: 20%, 50%, 100% and 150% of recommended N levels. A suite of optical, fluorescence, and biophysical measurements were collected on leaves from field grown corn (Zea mays L.) and soybean plants (Glycine max L.) grown in pots (greenhouse + ambient sunlight. Steady state laser-induced fluorescence emission spectra (5 nm resolution) were obtained from adaxial and abaxial surfaces resulting from excitation at single wavelengths (280, 380 or 360, and 532 nm). For emission spectra produced by each of these excitation wavelengths, ratios of emission peaks were calculated, including the red far-red chlorophyll fluorescence (ChlF) ratio (F685/F740) and the far-red/green (F740/F525) ratio. High resolution (< 3 nm) optical spectra (350-2500 nm) of reflectance, transmittance, and absorptance were also acquired for both adaxial and abaxial leaf surfaces. Species differences were demonstrated for several optical parameters. A 'red edge' derivative ratio determined from transmittance spectra [as the maximum first deivative, between 650-750 nm, normalized to the value at 744 nm, or Dmax/D744], was strongly associated with the C/N ratio (r(exp 2) = 0.90, P +/- 0.001). This ratio, calculated from reflectance spectra, was inversely related to chlorophyll b content (r(exp 2) = 0.91, P +/- 0.001) as was the ChlF (F685/F740) ratio obtained with 532 nm excitation (r(exp 2) = 0.76, P +/- 0.01). Discrimination of N treatment groups was possible with specific fluorescence band ratios (e.g., F740/F525 obtained with 380 nm excitation). Higher ChlF and blue-green emissions were measured from the abaxial leaf surfaces. Abaxial surfaces also produced higher reflectances, in general, in the 400-800 nm spectrum.

Scanning Laser Polarimetry and Optical Coherence Tomography for Detection of Retinal Nerve Fiber Layer Defects

PubMed Central

Oh, Jong-Hyun

2009-01-01

Purpose To compare the ability of scanning laser polarimetry with variable corneal compensation (GDx-VCC) and Stratus optical coherence tomography (OCT) to detect photographic retinal nerve fiber layer (RNFL) defects. Methods This retrospective cross-sectional study included 45 eyes of 45 consecutive glaucoma patients with RNFL defects in red-free fundus photographs. The superior and inferior temporal quadrants in each eye were included for data analysis separately. The location and presence of RNFL defects seen in red-free fundus photographs were compared with those seen in GDx-VCC deviation maps and OCT RNFL analysis maps for each quadrant. Results Of the 90 quadrants (45 eyes), 31 (34%) had no apparent RNFL defects, 29 (32%) had focal RNFL defects, and 30 (33%) had diffuse RNFL defects in red-free fundus photographs. The highest agreement between GDx-VCC and red-free photography was 73% when we defined GDx-VCC RNFL defects as a cluster of three or more color-coded squares (p<5%) along the traveling line of the retinal nerve fiber in the GDx-VCC deviation map (kappa value, 0.388; 95% confidence interval (CI), 0.195 to 0.582). The highest agreement between OCT and red-free photography was 85% (kappa value, 0.666; 95% CI, 0.506 to 0.825) when a value of 5% outside the normal limit for the OCT analysis map was used as a cut-off value for OCT RNFL defects. Conclusions According to the kappa values, the agreement between GDx-VCC deviation maps and red-free photography was poor, whereas the agreement between OCT analysis maps and red-free photography was good. PMID:19794943

ACCRETION RATES OF RED QUASARS FROM THE HYDROGEN Pβ LINE

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

Kim, Dohyeong; Im, Myungshin; Glikman, Eilat

Red quasars are thought to be an intermediate population between merger-driven star-forming galaxies in dust-enshrouded phase and normal quasars. If so, they are expected to have high accretion ratios, but their intrinsic dust extinction hampers reliable determination of Eddington ratios. Here, we compare the accretion rates of 16 red quasars at z ∼ 0.7 to those of normal type 1 quasars at the same redshift range. The red quasars are selected by their red colors in optical through near-infrared (NIR) and radio detection. The accretion rates of the red quasars are derived from the Pβ line in NIR spectra, whichmore » is obtained by the SpeX on the Infrared Telescope Facility in order to avoid the effects of dust extinction. We find that the measured Eddington ratios (L{sub bol}/L{sub Edd} ≃ 0.69) of red quasars are significantly higher than those of normal type 1 quasars, which is consistent with a scenario in which red quasars are the intermediate population and the black holes of red quasars grow very rapidly during such a stage.« less

Characterizations of individual human red blood cells from patients with diabetes mellitus (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lee, SangYun; Jang, Seongsoo; Park, HyunJoo; Park, YongKeun

2016-03-01

We systematically measure the morphological, biochemical, and biomechanical properties of individual human red blood cells (RBCs) from patients with diabetes mellitus using quantitative phase imaging technique to characterize the diabetic red cells with respect to those of the healthy. The 3-D refractive index tomograms and 2-D dynamic membrane fluctuation maps of individual RBCs are reconstructed from a set of the retrieved complex optical fields at various laser incidence angles using the Common-path diffraction optical tomography, from which volume, surface area, sphericity, hemoglobin (Hb) concentration, Hb content, and membrane fluctuation are obtained simultaneously. The correlative relations among the retrieved red cell indices of diabetic and healthy RBCs are also investigated with capabilities of individual cell measurement. As expected, there are no significant alterations in morphologies (cellular volumes, surface area, and sphericity) between diabetic and healthy RBCs. However, despite the minute mean corpuscular Hb differences in cell blood count datasheet, the measured Hb concentrations and Hb contents of diabetic RBCs are statistically higher than those of healthy RBCs, which might be related to the glycation of Hb molecules by hyperglycemia. Meanwhile, the membrane fluctuations of diabetic RBCs are clearly diminished compared to healthy red cells, implying the significantly decreased RBC deformability. In particular, it seems that the membrane fluctuations have mild negative relationships with the reported HbA1c levels.

Detecting the red tide based on remote sensing data in optically complex East China Sea

NASA Astrophysics Data System (ADS)

Xu, Xiaohui; Pan, Delu; Mao, Zhihua; Tao, Bangyi; Liu, Qiong

2012-09-01

Red tide not only destroys marine fishery production, deteriorates the marine environment, affects coastal tourist industry, but also causes human poison, even death by eating toxic seafood contaminated by red tide organisms. Remote sensing technology has the characteristics of large-scale, synchronized, rapid monitoring, so it is one of the most important and most effective means of red tide monitoring. This paper selects the high frequency red tides areas of the East China Sea as study area, MODIS/Aqua L2 data as the data source, analysis and compares the spectral differences in the red tide water bodies and non-red tide water bodies of many historical events. Based on the spectral differences, this paper develops the algorithm of Rrs555/Rrs488> 1.5 to extract the red tide information. Apply the algorithm on red tide event happened in the East China Sea on May 28, 2009 to extract the information of red tide, and found that the method can determine effectively the location of the occurrence of red tide; there is a good corresponding relationship between red tide extraction result and chlorophyll a concentration extracted by remote sensing, shows that these algorithm can determine effectively the location and extract the red tide information.

Microsatellite markers for northern red oak (Fagaceae: Quercus rubra)

Treesearch

Preston R. Aldrich; Charles H. Michler; Weilin Sun; Jeanne Romero-Severson

2002-01-01

We provide primer sequences for 14 (GA)n microsatellite loci developed from northern red oak, an important timber species. We screened loci using two sets of samples. A parent-offspring set included DNA from seven acorns collected from one mother tree along with maternal DNA, to determine that all progeny carried a maternal allele at each locus....

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

Geller, Aaron M.; Leiner, Emily M.; Mathieu, Robert D.

Sub-subgiants are stars that are observed to be redder than normal main-sequence stars and fainter than normal subgiant (and giant) stars in an optical color–magnitude diagram (CMD). The red straggler stars, which lie redward of the red giant branch, may be related and are often grouped together with the sub-subgiants in the literature. These stars defy our standard theory of single-star evolution and are important tests for binary evolution and stellar collision models. In total, we identify 65 sub-subgiants (SSG) and red stragglers (RS) in 16 open and globular star clusters from the literature; 50 of these, including 43 sub-subgiants,more » pass our strict membership selection criteria (though the remaining sources may also be cluster members). In addition to their unique location on the CMD, we find that at least 58% (25/43) of sub-subgiants in this sample are X-ray sources with typical 0.5–2.5 keV luminosities of order 10{sup 30}–10{sup 31} erg s{sup −1}. Their X-ray luminosities and optical–to–X-ray flux ratios are similar to those of RS CVn active binaries. At least 65% (28/43) of the sub-subgiants in our sample are variables, 21 of which are known to be radial-velocity binaries. Typical variability periods are ≲15 days. At least 33% (14/43) of the sub-subgiants are H α emitters. These observational demographics provide strong evidence that binarity is important for sub-subgiant formation. Finally, we find that the number of sub-subgiants per unit mass increases toward lower-mass clusters, such that the open clusters in our sample have the highest specific frequencies of sub-subgiants.« less

TESTING SCALING RELATIONS FOR SOLAR-LIKE OSCILLATIONS FROM THE MAIN SEQUENCE TO RED GIANTS USING KEPLER DATA

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

Huber, D.; Bedding, T. R.; Stello, D.

2011-12-20

We have analyzed solar-like oscillations in {approx}1700 stars observed by the Kepler Mission, spanning from the main sequence to the red clump. Using evolutionary models, we test asteroseismic scaling relations for the frequency of maximum power ({nu}{sub max}), the large frequency separation ({Delta}{nu}), and oscillation amplitudes. We show that the difference of the {Delta}{nu}-{nu}{sub max} relation for unevolved and evolved stars can be explained by different distributions in effective temperature and stellar mass, in agreement with what is expected from scaling relations. For oscillation amplitudes, we show that neither (L/M){sup s} scaling nor the revised scaling relation by Kjeldsen andmore » Bedding is accurate for red-giant stars, and demonstrate that a revised scaling relation with a separate luminosity-mass dependence can be used to calculate amplitudes from the main sequence to red giants to a precision of {approx}25%. The residuals show an offset particularly for unevolved stars, suggesting that an additional physical dependency is necessary to fully reproduce the observed amplitudes. We investigate correlations between amplitudes and stellar activity, and find evidence that the effect of amplitude suppression is most pronounced for subgiant stars. Finally, we test the location of the cool edge of the instability strip in the Hertzsprung-Russell diagram using solar-like oscillations and find the detections in the hottest stars compatible with a domain of hybrid stochastically excited and opacity driven pulsation.« less

β-Octakis(methylthio)porphycenes: synthesis, characterisation and third order nonlinear optical studies.

PubMed

Rana, Anup; Lee, Sangsu; Kim, Dongho; Panda, Pradeepta K

2015-05-04

A novel electron deficient β-octakis(methylthio)porphycene, along with its Zn(ii) and Ni(ii) derivatives, was synthesized for the first time. The macrocyclic structure exhibits core ruffling with a largely red shifted absorption band (∼750 nm) and also a large enhancement in the third order nonlinear optical response.

Evaluating a novel application of optical fibre evanescent field absorbance: rapid measurement of red colour in winegrape homogenates

NASA Astrophysics Data System (ADS)

Lye, Peter G.; Bradbury, Ronald; Lamb, David W.

Silica optical fibres were used to measure colour (mg anthocyanin/g fresh berry weight) in samples of red wine grape homogenates via optical Fibre Evanescent Field Absorbance (FEFA). Colour measurements from 126 samples of grape homogenate were compared against the standard industry spectrophotometric reference method that involves chemical extraction and subsequent optical absorption measurements of clarified samples at 520 nm. FEFA absorbance on homogenates at 520 nm (FEFA520h) was correlated with the industry reference method measurements of colour (R2 = 0.46, n = 126). Using a simple regression equation colour could be predicted with a standard error of cross-validation (SECV) of 0.21 mg/g, with a range of 0.6 to 2.2 mg anthocyanin/g and a standard deviation of 0.33 mg/g. With a Ratio of Performance Deviation (RPD) of 1.6, the technique when utilizing only a single detection wavelength, is not robust enough to apply in a diagnostic sense, however the results do demonstrate the potential of the FEFA method as a fast and low-cost assay of colour in homogenized samples.

Investigation on dynamics of red blood cells through their behavior as biophotonic lenses.

PubMed

Memmolo, Pasquale; Merola, Francesco; Miccio, Lisa; Mugnano, Martina; Ferraro, Pietro

2016-12-01

The possibility to adopt biological matter as photonic optical elements can open scenarios in biophotonics research. Recently, it has been demonstrated that a red blood cell (RBC) can be seen as an optofluidic microlens by showing its imaging capability as well as its focal tunability. Moreover, correlation between an RBC’s morphology and its behavior as a refractive optical element has been established and its exploitation for biomedical diagnostic purposes has been foreseen. In fact, any deviation from the healthy RBC morphology can be seen as additional aberration in the optical wavefront passing through the cell. By this concept, accurate localization of focal spots of RBCs can become very useful in the blood disorders identification. We investigate the three-dimensional positioning of such focal spots over time for samples with two different osmolarity conditions, i.e., when they assume discocyte and spherical shapes, respectively. We also demonstrate that a temporal variation of an RBC’s focal points along the optical axis is correlated to the temporal fluctuations in the RBC’s thickness maps. Furthermore, we show a sort of synchronization of the whole erythrocytes ensemble.

Cermet based metamaterials for multi band absorbers over NIR to LWIR frequencies

NASA Astrophysics Data System (ADS)

Pradhan, Jitendra K.; Behera, Gangadhar; Agarwal, Amit K.; Ghosh, Amitava; Ramakrishna, S. Anantha

2017-06-01

Cermets or ceramic-metals are known for their use in solar thermal technologies for their absorption across the solar band. Use of cermet layers in a metamaterial perfect absorber allows for flexible control of infra-red absorption over the short wave infra-red, to long wave infra-red bands, while keeping the visible/near infra-red absorption properties constant. We design multilayered metamaterials consisting of a conducting ground plane, a low metal volume fraction cermet/ZnS as dielectric spacer layers, and a top structured layer of an array of circular discs of metal/high volume metal fraction cermet that give rise to specified absorption bands in the near-infra-red (NIR) frequencies, as well as any specified band at SWIR-LWIR frequencies. Thus, a complete decoupling of the absorption at optical/NIR frequencies and the infra-red absorption behaviour of a structured metamaterial is demonstrated.

High-speed all-optical DNA local sequence alignment based on a three-dimensional artificial neural network.

PubMed

Maleki, Ehsan; Babashah, Hossein; Koohi, Somayyeh; Kavehvash, Zahra

2017-07-01

This paper presents an optical processing approach for exploring a large number of genome sequences. Specifically, we propose an optical correlator for global alignment and an extended moiré matching technique for local analysis of spatially coded DNA, whose output is fed to a novel three-dimensional artificial neural network for local DNA alignment. All-optical implementation of the proposed 3D artificial neural network is developed and its accuracy is verified in Zemax. Thanks to its parallel processing capability, the proposed structure performs local alignment of 4 million sequences of 150 base pairs in a few seconds, which is much faster than its electrical counterparts, such as the basic local alignment search tool.

Pulsed near-infrared photoacoustic spectroscopy of blood

NASA Astrophysics Data System (ADS)

Laufer, Jan G.; Elwell, Clare E.; Delpy, Dave T.; Beard, Paul C.

2004-07-01

The aim of this study was to use pulsed near infrared photoacoustic spectroscopy to determine the oxygen saturation (SO2) of a saline suspension of red blood cells in vitro. The photoacoustic measurements were made in a cuvette which formed part of a larger circuit through which the red blood cell suspension was circulated. Oxygen saturation of the red blood cell suspension was altered between 2-3% to 100% in step increments using a membrane oxygenator and at each increment an independent measurement of oxygen saturation was made using a co-oximeter. An optical parametric oscillator laser system provided nanosecond excitation pulses at a number of wavelengths in the near-infrared spectrum (740-1040nm) which were incident on the cuvette. The resulting acoustic signals were detected using a broadband (15MHz) Fabry-Perot polymer film transducer. The optical transport coefficient and amplitude were determined from the acoustic signals as a function of wavelength. These data were then used to calculate the relative concentrations of oxy- and deoxyhaemoglobin, using their known specific absorption coefficients and an empirically determined wavelength dependence of optical scattering over the wavelength range investigated. From this, the oxygen saturation of the suspension was derived with an accuracy of +/-5% compared to the co-oximeter SO2 measurements.

Tuning Ag29 nanocluster light emission from red to blue with one and two-photon excitation.

PubMed

Russier-Antoine, Isabelle; Bertorelle, Franck; Hamouda, Ramzi; Rayane, Driss; Dugourd, Philippe; Sanader, Željka; Bonačić-Koutecký, Vlasta; Brevet, Pierre-François; Antoine, Rodolphe

2016-02-07

We demonstrate that the tuning of the light emission from red to blue in dihydrolipoic acid (DHLA) capped Ag29 nanoclusters can be trigged with one and two photon excitations. The cluster stoichiometry was determined with mass spectrometry and found to be Ag29(DHLA)12. In a detailed optical investigation, we show that these silver nanoclusters exhibit a strong red photoluminescence visible to the naked eye and characterized by a quantum yield of nearly ∼2% upon one-photon excitation. In the nonlinear optical (NLO) study of the properties of the clusters, the two-photon excited fluorescence spectra were recorded and their first hyperpolarizability obtained. The two-photon absorption cross-section at ∼800 nm for Ag29(DHLA)12 is higher than 10(4) GM and the hyperpolarizability is 106 × 10(-30) esu at the same excitation wavelength. The two-photon excited fluorescence spectrum appears strongly blue-shifted as compared to the one-photon excited spectrum, displaying a broad band between 400 and 700 nm. The density functional theory (DFT) provides insight into the structural and electronic properties of Ag29(DHLA)12 as well as into interplay between metallic subunit or core and ligands which is responsible for unique optical properties.

RGB and white-emitting organic lasers on flexible glass.

PubMed

Foucher, C; Guilhabert, B; Kanibolotsky, A L; Skabara, P J; Laurand, N; Dawson, M D

2016-02-08

Two formats of multiwavelength red, green and blue (RGB) laser on mechanically-flexible glass are demonstrated. In both cases, three all-organic, vertically-emitting distributed feedback (DFB) lasers are assembled onto a common ultra-thin glass membrane substrate and fully encapsulated by a thin polymer overlayer and an additional 50 µm-thick glass membrane in order to improve the performance. The first device format has the three DFB lasers sitting next to each other on the glass substrate. The DFB lasers are simultaneously excited by a single overlapping optical pump, emitting spatially separated red, green and blue laser output with individual thresholds of, respectively, 28 µJ/cm(2), 11 µJ/cm(2) and 32 µJ/cm(2) (for 5 ns pump pulses). The second device format has the three DFB lasers, respectively the red, green and blue laser, vertically stacked onto the flexible glass. This device format emits a white laser output for an optical pump fluence above 42 µJ/cm(2).

Ultraviolet and optical observations of metal deficient red giants and chromospheric models

NASA Technical Reports Server (NTRS)

Duprele, A. K.; Avrett, E. H.; Hartmann, L.; Smith, G.

1984-01-01

Three metal deficient field stars were observed in the ultraviolet and optical spectral regions: HD 165195, HD 110281, and HD 232078. High dispersion spectra near H alpha, and low dispersion, long wavelength IUE spectra were obtained. The H alpha profiles have strong asymmetric emission with absorption cores that are frequently asymmetric. The surface flux of Mg II lines is similar to that of luminous Pop I stars in spite of the lower metal abundance. Semi-empirical atmospheric models suggest that the characteristic emission in the wings of the H alpha line can arise within static chromospheres. Radial expansion gives an asymmetric, blue-shifted H alpha core accompanied by greater emission in the red line wing than the blue wing. Wind models with extended atmospheres suggest mass loss rates - 2 billion M/yr. Thus H alpha provides no evidence that steady mass loss is substantial enough to significantly affect the evolution of stars on the red giant branch of globular clusters.

Delocalization of frontier orbitals induced red emission for heptazine based thermally activated delayed fluorescence molecule: First-principles study

NASA Astrophysics Data System (ADS)

Kang, Yongxiang; Zhao, Liyun; Leng, Jiancai

2018-04-01

Design of red organic emitting molecules with characteristic of thermally activated delayed fluorescence (TADF) remains a great challenge. Here, electronic and optical properties of a series of multi-branched TADF molecules have been investigated based on the newly-proposed optimal Hartree-Fock percentage method. Results show that, though enlarging the delocalization of HOMO and LUMO, the emission wavelength is redshift. The designed red TADF molecule possesses smaller reorganization energy than these for reported molecules. This indicates the non-radiative energy consumption of excited state is small and effective luminescence can be expected. Thus, a promising red thermally activated delayed fluorescence molecule is proposed.

Bio-optical characteristics of a red tide induced by Mesodinium rubrum in the Cariaco Basin, Venezuela

NASA Astrophysics Data System (ADS)

Guzmán, Laurencia; Varela, Ramón; Muller-Karger, Frank; Lorenzoni, Laura

2016-08-01

The bio-optical changes of the water induced by red tides depend on the type of organism present, and the spectral characterization of such changes can provide useful information on the organism, abundance and distribution. Here we present results from the bio-optical characterization of a non-toxic red tide induced by the autotrophic ciliate Mesodinium rubrum. Particle absorption was high [ap(440) = 1.78 m- 1], as compared to measurements done in the same region [ap(440) = 0.09 ± 0.06 m- 1], with detrital components contributing roughly 11% [ad(440) = 0.19 m- 1]. The remainder was attributed to absorption by phytoplankton pigments [aph(440) = 1.60 m- 1]. These aph values were ~ 15 times higher than typical values for these waters. High chlorophyll a concentrations were also measured (52.73 μg L- 1), together with alloxanthin (9.52 μg L- 1) and chlorophyll c (6.25 μg L- 1). This suite of pigment is typical of the algal class Cryptophyceae, from which Mesodinium obtains its chloroplasts. Remote sensing reflectance showed relatively low values [Rrs(440) = 0.0007 sr- 1], as compared to other Rrs values for the region under high bloom conditions [Rrs(440) = 0.0028 sr- 1], with maxima at 388, 484, 520, 596 and 688 nm. Based on the low reflection in the green-yellow, as compared to other red tides, we propose a new band ratio [Rrs(688)/Rrs(564)] to identify blooms of this particular group of organisms.

Co-Precipitation Synthesis and Optical Properties of Mn4+-Doped Hexafluoroaluminate w-LED Phosphors

PubMed Central

Geitenbeek, Robin G.; Meijerink, Andries

2017-01-01

Mn4+-activated hexafluoroaluminates are promising red-emitting phosphors for white light emitting diodes (w-LEDs). Here, we report the synthesis of Na3AlF6:Mn4+, K3AlF6:Mn4+ and K2NaAlF6:Mn4+ phosphors through a simple two-step co-precipitation method. Highly monodisperse large (~20 μm) smoothed-octahedron shaped crystallites are obtained for K2NaAlF6:Mn4+. The large size, regular shape and small size distribution are favorable for application in w-LEDs. All Mn4+-doped hexafluoroaluminates show bright red Mn4+ luminescence under blue light excitation. We compare the optical properties of Na3AlF6:Mn4+, K3AlF6:Mn4+ and K2NaAlF6:Mn4+ at room temperature and 4 K. The luminescence measurements reveal that multiple Mn4+ sites exist in M3AlF6:Mn4+ (M = Na, K), which is explained by the charge compensation that is required for Mn4+ on Al3+ sites. Thermal cycling experiments show that the site distribution changes after annealing. Finally, we investigate thermal quenching and show that the luminescence quenching temperature is high, around 460–490 K, which makes these Mn4+-doped hexafluoroaluminates interesting red phosphors for w-LEDs. The new insights reported on the synthesis and optical properties of Mn4+ in the chemically and thermally stable hexafluoroaluminates can contribute to the optimization of red-emitting Mn4+ phosphors for w-LEDs. PMID:29149083

A single population of red globular clusters around the massive compact galaxy NGC 1277

NASA Astrophysics Data System (ADS)

Beasley, Michael A.; Trujillo, Ignacio; Leaman, Ryan; Montes, Mireia

2018-03-01

Massive galaxies are thought to form in two phases: an initial collapse of gas and giant burst of central star formation, followed by the later accretion of material that builds up their stellar and dark-matter haloes. The systems of globular clusters within such galaxies are believed to form in a similar manner. The initial central burst forms metal-rich (spectrally red) clusters, whereas more metal-poor (spectrally blue) clusters are brought in by the later accretion of less-massive satellites. This formation process is thought to result in the multimodal optical colour distributions that are seen in the globular cluster systems of massive galaxies. Here we report optical observations of the massive relic-galaxy candidate NGC 1277—a nearby, un-evolved example of a high-redshift ‘red nugget’ galaxy. We find that the optical colour distribution of the cluster system of NGC 1277 is unimodal and entirely red. This finding is in strong contrast to other galaxies of similar and larger stellar mass, the cluster systems of which always exhibit (and are generally dominated by) blue clusters. We argue that the colour distribution of the cluster system of NGC 1277 indicates that the galaxy has undergone little (if any) mass accretion after its initial collapse, and use simulations of possible merger histories to show that the stellar mass due to accretion is probably at most ten per cent of the total stellar mass of the galaxy. These results confirm that NGC 1277 is a genuine relic galaxy and demonstrate that blue clusters constitute an accreted population in present-day massive galaxies.

A single population of red globular clusters around the massive compact galaxy NGC 1277.

PubMed

Beasley, Michael A; Trujillo, Ignacio; Leaman, Ryan; Montes, Mireia

2018-03-22

Massive galaxies are thought to form in two phases: an initial collapse of gas and giant burst of central star formation, followed by the later accretion of material that builds up their stellar and dark-matter haloes. The systems of globular clusters within such galaxies are believed to form in a similar manner. The initial central burst forms metal-rich (spectrally red) clusters, whereas more metal-poor (spectrally blue) clusters are brought in by the later accretion of less-massive satellites. This formation process is thought to result in the multimodal optical colour distributions that are seen in the globular cluster systems of massive galaxies. Here we report optical observations of the massive relic-galaxy candidate NGC 1277-a nearby, un-evolved example of a high-redshift 'red nugget' galaxy. We find that the optical colour distribution of the cluster system of NGC 1277 is unimodal and entirely red. This finding is in strong contrast to other galaxies of similar and larger stellar mass, the cluster systems of which always exhibit (and are generally dominated by) blue clusters. We argue that the colour distribution of the cluster system of NGC 1277 indicates that the galaxy has undergone little (if any) mass accretion after its initial collapse, and use simulations of possible merger histories to show that the stellar mass due to accretion is probably at most ten per cent of the total stellar mass of the galaxy. These results confirm that NGC 1277 is a genuine relic galaxy and demonstrate that blue clusters constitute an accreted population in present-day massive galaxies.

Whispering Gallery Optical Resonator Spectroscopic Probe and Method

NASA Technical Reports Server (NTRS)

Anderson, Mark S. (Inventor)

2014-01-01

Disclosed herein is a spectroscopic probe comprising at least one whispering gallery mode optical resonator disposed on a support, the whispering gallery mode optical resonator comprising a continuous outer surface having a cross section comprising a first diameter and a second diameter, wherein the first diameter is greater than the second diameter. A method of measuring a Raman spectrum and an Infra-red spectrum of an analyte using the spectroscopic probe is also disclosed.

Combining Optical Reporter Proteins with Different Half-lives to Detect Temporal Evolution of Hypoxia and Reoxygenation in Tumors.

PubMed

Danhier, Pierre; Krishnamachary, Balaji; Bharti, Santosh; Kakkad, Samata; Mironchik, Yelena; Bhujwalla, Zaver M

2015-12-01

Here we have developed a hypoxia response element driven imaging strategy that combined the hypoxia-driven expression of two optical reporters with different half-lives to detect temporal changes in hypoxia and hypoxia inducible factor (HIF) activity. For this purpose, human prostate cancer PC3 cells were transfected with the luciferase gene fused with an oxygen-dependent degradation domain (ODD-luc) and a variant of the enhanced green fluorescent protein (EGFP). Both ODD-luciferase and EGFP were under the promotion of a poly-hypoxia-response element sequence (5xHRE). The cells constitutively expressed tdTomato red fluorescent protein. For validating the imaging strategy, cells were incubated under hypoxia (1% O2) for 48 hours and then reoxygenated. The luciferase activity of PC3-HRE-EGFP/HRE-ODD-luc/tdtomato cells detected by bioluminescent imaging rapidly decreased after reoxygenation, whereas EGFP levels in these cells remained stable for several hours. After in vitro validation, PC3-HRE-EGFP/HRE-ODD-luc/tdtomato tumors were implanted subcutaneously and orthotopically in nude male mice and imaged in vivo and ex vivo using optical imaging in proof-of-principle studies to demonstrate differences in optical patterns between EGFP expression and bioluminescence. This novel "timer" imaging strategy of combining the short-lived ODD-luciferase and the long-lived EGFP can provide a time frame of HRE activation in PC3 prostate cancer cells and will be useful to understand the temporal changes in hypoxia and HIF activity during cancer progression and following treatments including HIF targeting strategies. Copyright © 2015 Nencki Institute of Experimental Biology, Polish Academy of Sciences,. Published by Elsevier Inc. All rights reserved.

THE SWIFT AGN AND CLUSTER SURVEY. II. CLUSTER CONFIRMATION WITH SDSS DATA

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

Griffin, Rhiannon D.; Dai, Xinyu; Kochanek, Christopher S.

2016-01-15

We study 203 (of 442) Swift AGN and Cluster Survey extended X-ray sources located in the SDSS DR8 footprint to search for galaxy over-densities in three-dimensional space using SDSS galaxy photometric redshifts and positions near the Swift cluster candidates. We find 104 Swift clusters with a >3σ galaxy over-density. The remaining targets are potentially located at higher redshifts and require deeper optical follow-up observations for confirmation as galaxy clusters. We present a series of cluster properties including the redshift, brightest cluster galaxy (BCG) magnitude, BCG-to-X-ray center offset, optical richness, and X-ray luminosity. We also detect red sequences in ∼85% ofmore » the 104 confirmed clusters. The X-ray luminosity and optical richness for the SDSS confirmed Swift clusters are correlated and follow previously established relations. The distribution of the separations between the X-ray centroids and the most likely BCG is also consistent with expectation. We compare the observed redshift distribution of the sample with a theoretical model, and find that our sample is complete for z ≲ 0.3 and is still 80% complete up to z ≃ 0.4, consistent with the SDSS survey depth. These analysis results suggest that our Swift cluster selection algorithm has yielded a statistically well-defined cluster sample for further study of cluster evolution and cosmology. We also match our SDSS confirmed Swift clusters to existing cluster catalogs, and find 42, 23, and 1 matches in optical, X-ray, and Sunyaev–Zel’dovich catalogs, respectively, and so the majority of these clusters are new detections.« less

High-speed optical phase-shifting apparatus

DOEpatents

Zortman, William A.

2016-11-08

An optical phase shifter includes an optical waveguide, a plurality of partial phase shifting elements arranged sequentially, and control circuitry electrically coupled to the partial phase shifting elements. The control circuitry is adapted to provide an activating signal to each of the N partial phase shifting elements such that the signal is delayed by a clock cycle between adjacent partial phase shifting elements in the sequence. The transit time for a guided optical pulse train between the input edges of consecutive partial phase shifting elements in the sequence is arranged to be equal to a clock cycle, thereby enabling pipelined processing of the optical pulses.

Bilateral Optic Disc Drusen Mimicking Papilledema

PubMed Central

Cingü, Abdullah Kürşat; Ari, Şeyhmus; Çinar, Yasin; Çaça, İhsan

2012-01-01

Background Optic disc drusen, which are calcified deposits that form anterior to the lamina cribrosa in the optic nerve, may mimic papilledema. Case Report We report herein three cases referred to us with suspicion of disc swelling and papilledema. Following ophthalmologic evaluation with B-scan ultrasound, red-free fundus photography, and computed tomography, the diagnosis of papilledema was excluded in all cases and optic disc drusen was diagnosed. Conclusions Clinical suspicion of optic disc drusen in cases presenting with swelling of the optic nerve head is important in order to avoid unnecessary interventions and anxiety. The reported cases highlight the commonly encountered clinical presentations and the practical aspects of diagnosis and management of optic disc drusen. PMID:22787500

Sequence and phylogenetic analyses of novel totivirus-like double-stranded RNAs from field-collected powdery mildew fungi.

PubMed

Kondo, Hideki; Hisano, Sakae; Chiba, Sotaro; Maruyama, Kazuyuki; Andika, Ida Bagus; Toyoda, Kazuhiro; Fujimori, Fumihiro; Suzuki, Nobuhiro

2016-02-02

The identification of mycoviruses contributes greatly to understanding of the diversity and evolutionary aspects of viruses. Powdery mildew fungi are important and widely studied obligate phytopathogenic agents, but there has been no report on mycoviruses infecting these fungi. In this study, we used a deep sequencing approach to analyze the double-stranded RNA (dsRNA) segments isolated from field-collected samples of powdery mildew fungus-infected red clover plants in Japan. Database searches identified the presence of at least ten totivirus (genus Totivirus)-like sequences, termed red clover powdery mildew-associated totiviruses (RPaTVs). The majority of these sequences shared moderate amino acid sequence identity with each other (<44%) and with other known totiviruses (<59%). Nine of these identified sequences (RPaTV1a, 1b and 2-8) resembled the genome of the prototype totivirus, Saccharomyces cerevisiae virus-L-A (ScV-L-A) in that they contained two overlapping open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA dependent RNA polymerase (RdRp), while one sequence (RPaTV9) showed similarity to another totivirus, Ustilago maydis virus H1 (UmV-H1) that encodes a single polyprotein (CP-RdRp fusion). Similar to yeast totiviruses, each ScV-L-A-like RPaTV contains a -1 ribosomal frameshift site downstream of a predicted pseudoknot structure in the overlapping region of these ORFs, suggesting that the RdRp is translated as a CP-RdRp fusion. Moreover, several ScV-L-A-like sequences were also found by searches of the transcriptome shotgun assembly (TSA) libraries from rust fungi, plants and insects. Phylogenetic analyses show that nine ScV-L-A-like RPaTVs along with ScV-L-A-like sequences derived from TSA libraries are clustered with most established members of the genus Totivirus, while one RPaTV forms a new distinct clade with UmV-H1, possibly establishing an additional genus in the family. Taken together, our results indicate the presence of diverse, novel totiviruses in the powdery mildew fungus populations infecting red clover plants in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

Whence the red panda?

PubMed

Flynn, J J; Nedbal, M A; Dragoo, J W; Honeycutt, R L

2000-11-01

The evolutionary history of the red panda (Ailurus fulgens) plays a pivotal role in the higher-level phylogeny of the "bear-like" arctoid carnivoran mammals. Characters from morphology and molecules have provided inconsistent evidence for placement of the red panda. Whereas it certainly is an arctoid, there has been major controversy about whether it should be placed with the bears (ursids), ursids plus pinnipeds (seals, sea lions, walrus), raccoons (procyonids), musteloids (raccoons plus weasels, skunks, otters, and badgers [mustelids]), or as a monotypic lineage of uncertain phylogenetic affinities. Nucleotide sequence data from three mitochondrial genes and one nuclear intron were analyzed, with more complete taxonomic sampling of relevant taxa (arctoids) than previously available in analyses of primary molecular data, to clarify the phylogenetic relationships of the red panda to other arctoid carnivorans. This study provides detailed phylogenetic analyses (both parsimony and maximum-likelihood) of primary character data for arctoid carnivorans, including bootstrap and decay indices for all arctoid nodes, and three statistical tests of alternative phylogenetic hypotheses for the placement of the red panda. Combined phylogenetic analyses reject the hypotheses that the red panda is most closely related to the bears (ursids) or to the raccoons (procyonids). Rather, evidence from nucleotide sequences strongly support placement of the red panda within a broad Musteloidea (sensu lato) clade, including three major lineages (the red panda, the skunks [mephitids], and a clearly monophyletic clade of procyonids plus mustelids [sensu stricto, excluding skunks]). Within the Musteloidea, interrelationships of the three major lineages are unclear and probably are best considered an unresolved trichotomy. These data provide compelling evidence for the relationships of the red panda and demonstrate that small taxonomic sample sizes can result in misleading or possibly erroneous (based on prior modeling, as well as conflict between the results of our analyses of less and more complete data sets) conclusions about phylogenetic relationships and taxonomy. Copyright 2000 Academic Press.

Multigene panel next generation sequencing in a patient with cherry red macular spot: Identification of two novel mutations in NEU1 gene causing sialidosis type I associated with mild to unspecific biochemical and enzymatic findings.

PubMed

Mütze, Ulrike; Bürger, Friederike; Hoffmann, Jessica; Tegetmeyer, Helmut; Heichel, Jens; Nickel, Petra; Lemke, Johannes R; Syrbe, Steffen; Beblo, Skadi

2017-03-01

Lysosomal storage diseases (LSD) often manifest with cherry red macular spots. Diagnosis is based on clinical features and specific biochemical and enzymatic patterns. In uncertain cases, genetic testing with next generation sequencing can establish a diagnosis, especially in milder or atypical phenotypes. We report on the diagnostic work-up in a boy with sialidosis type I, presenting initially with marked cherry red macular spots but non-specific urinary oligosaccharide patterns and unusually mild excretion of bound sialic acid. Biochemical, enzymatic and genetic tests were performed in the patient. The clinical and electrophysiological data was reviewed and a genotype-phenotype analysis was performed. In addition a systematic literature review was carried out. Cherry red macular spots were first noted at 6 years of age after routine screening myopia. Physical examination, psychometric testing, laboratory investigations as well as cerebral MRI were unremarkable at 9 years of age. So far no clinical myoclonic seizures occurred, but EEG displays generalized epileptic discharges and visual evoked potentials are prolonged bilaterally. Urine thin layer chromatography showed an oligosaccharide pattern compatible with different LSD including sialidosis, galactosialidosis, GM1 gangliosidosis or mucopolysaccharidosis type IV B. Urinary bound sialic acid excretion was mildly elevated in spontaneous and 24 h urine samples. In cultured fibroblasts, α-sialidase activity was markedly decreased to < 1%; however, bound and free sialic acid were within normal range. Diagnosis was eventually established by multigene panel next generation sequencing of genes associated to LSD, identifying two novel, compound heterozygous variants in NEU1 gene (c.699C > A, p.S233R in exon 4 and c.803A > G; p.Y268C in Exon 5 in NEU1 transcript NM_000434.3), leading to amino acid changes predicted to impair protein function. Sialidosis should be suspected in patients with cherry red macular spots, even with non-significant urinary sialic acid excretion. Multigene panel next generation sequencing can establish a definite diagnosis, allowing for counseling of the patient and family.

Coastal Secchi Depth Atlas

DTIC Science & Technology

1985-07-01

ptical properties 5pley. I(-,8). Table 5. Chart 4-Percentage of one-degree squares. 13 f plankton aleae . 0 Table 6. Global coverage-Percentage of one...optical properties result from (e.g., Colorado River), typical in mountainous (tectonic) regions, 9. Hunghlo (Red)110 Mekong and/or organic sediments...typical in mountainous (tectonic) regions, 9. Hungho (Red) 160 Inadequate 10. Mekong 160 Sufficient larger-sized particles in suspension. The

Shell-Type Micromechanical Oscillator

DTIC Science & Technology

2003-04-01

interferometric setup. A positive feedback loop was implemented by amplifying the red laser signal (related to the oscillator deflection) and using...resonator was actuated by a sharply focused, modulated Ar+ ion (blue) laser beam and detected by a red HeNe laser using an interferometric setup. A positive...top. Fig. 1 shows optical micrograph obtained by DIC (Differential Interference Contrast, known also as Nomarsky contrast). An array of three domes

Characterization of malaria infected blood cells by scanning confocal laser and acoustic vector contrast microscopy

NASA Astrophysics Data System (ADS)

Ahmed Mohamed, E. T.; Schubert, S.; Gilberger, T. W.; Kamanyi, A., Jr.; Wannemacher, R.; Grill, W.

2006-03-01

Acoustic and optical multiple contrast microscopy has been employed in order to explore characterizable parameters of red blood cells, including cells infected by the parasite Plasmodium falciparum, in order to investigate cellular modifications caused by the infection and to identify possible detection schemes for disease monitoring. Imaging schemes were based on fluorescence, optical transmission, optical reflection, and amplitude and phase of ultrasound reflected from the cells. Contrast variations observed in acoustic microscopy, but not in optical microscopy, were tentatively ascribed to changes caused by the infection.

Shotgun Optical Maps of the Whole Escherichia coli O157:H7 Genome

PubMed Central

Lim, Alex; Dimalanta, Eileen T.; Potamousis, Konstantinos D.; Yen, Galex; Apodoca, Jennifer; Tao, Chunhong; Lin, Jieyi; Qi, Rong; Skiadas, John; Ramanathan, Arvind; Perna, Nicole T.; Plunkett, Guy; Burland, Valerie; Mau, Bob; Hackett, Jeremiah; Blattner, Frederick R.; Anantharaman, Thomas S.; Mishra, Bhubaneswar; Schwartz, David C.

2001-01-01

We have constructed NheI and XhoI optical maps of Escherichia coli O157:H7 solely from genomic DNA molecules to provide a uniquely valuable scaffold for contig closure and sequence validation. E. coli O157:H7 is a common pathogen found in contaminated food and water. Our approach obviated the need for the analysis of clones, PCR products, and hybridizations, because maps were constructed from ensembles of single DNA molecules. Shotgun sequencing of bacterial genomes remains labor-intensive, despite advances in sequencing technology. This is partly due to manual intervention required during the last stages of finishing. The applicability of optical mapping to this problem was enhanced by advances in machine vision techniques that improved mapping throughput and created a path to full automation of mapping. Comparisons were made between maps and sequence data that characterized sequence gaps and guided nascent assemblies. PMID:11544203

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

USDA-ARS?s Scientific Manuscript database

Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker d...

Reconnaissance geologic map of the Muwassam Quadrangle, sheet 16/42 D, Kingdom of Saudi Arabia

USGS Publications Warehouse

Blank, H. Richard

1985-01-01

All of the mapped area is occupied by coastal plain bordering the Red Sea. The flat coastal plain is covered by Quaternary surficial deposits overlying a sequence of Tertiary rocks as much as 5 km thick. The coastal plain is separated from the Red Sea by zone of supratidal sabkha deposits, offshore bars, islands, tidal md flats, and shallow lagoons. The sea is shallow, less than 200 m deep, and forms part of the shelf marginal to the main axial trough of the Red Sea.

Use of Simple Sequence Repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp.) cultivars resistant and susceptible to red rot

USDA-ARS?s Scientific Manuscript database

In recent years SSR markers have been used widely for the genetic analysis. The objective of present research was to use SSR markers to develop DNA-based genetic identification and analyze genetic relationship of sugarcane cultivars grown in Pakistan either resistant or susceptible to red rot. Twent...

Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach.

PubMed

Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

2015-07-01

Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR-RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. PCR-RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR-RED. NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR-RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 John Wiley & Sons, Ltd.

First Molecular Characterization of Hypoderma actaeon in Cattle and Red Deer (Cervus elaphus) in Portugal.

PubMed

Ahmed, Haroon; Sousa, Sérgio Ramalho; Simsek, Sami; Anastácio, Sofia; Kilinc, Seyma Gunyakti

2017-12-01

Hypoderma spp. larvae cause subcutaneous myiasis in several animal species. The objective of the present investigation was to identify and characterize morphologically and molecularly the larvae of Hypoderma spp. collected from cattle (Bos taurus taurus) and red deer (Cervus elaphus) in the district of Castelo Branco, Portugal. For this purpose, a total of 8 larvae were collected from cattle (n=2) and red deer (n=6). After morphological identification of Hypoderma spp. larvae, molecular characterization was based on PCR-RFLP and mitochondrial CO1 gene sequence analysis. All larvae were morphologically characterized as the third instar larvae (L3) of H. actaeon. Two restriction enzymes were used for molecular identification of the larvae. TaqI restriction enzyme was not able to cut H. actaeon. However, MboII restriction enzyme differentiated Hypoderma species showing 210 and 450 bp bands in H. actaeon. Furthermore, according to the alignment of the mt-CO1 gene sequences of Hypoderma species and to PCR-RFLP findings, all the identified Hypoderma larvae were confirmed as H. actaeon. This is the first report of identification of Hypoderma spp. (Diptera; Oestridae) from cattle and red deer in Portugal, based on morphological and molecular analyses.

Distribution and diversity of Prochlorococcus ecotypes in the Red Sea.

PubMed

Shibl, Ahmed A; Thompson, Luke R; Ngugi, David K; Stingl, Ulrich

2014-07-01

Photosynthetic prokaryotes of the genus Prochlorococcus play a major role in global primary production in the world's oligotrophic oceans. A recent study on pelagic bacterioplankton communities in the northern and central Red Sea indicated that the predominant cyanobacterial 16S rRNA gene sequence types were from Prochlorococcus cells belonging to a high-light-adapted ecotype (HL II). In this study, we analyzed microdiversity of Prochlorococcus sp. at multiple depths within and below the euphotic zone in the northern, central, and southern regions of the Red Sea, as well as in surface waters in the same locations, but in a different season. Prochlorococcus dominated the communities in clone libraries of the amplified 16S-23S rRNA internal transcribed spacer (ITS) region. Almost no differences were found between samples from coastal or open-water sites, but a high diversity of Prochlorococcus ecotypes was detected at 100-meter depth in the water column. In addition, an unusual dominance of HL II-related sequences was observed in deeper waters. Our results indicate that the Red Sea harbors diverse Prochlorococcus lineages, but no novel ecotypes, despite its unusual physicochemical properties. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Using optical mapping data for the improvement of vertebrate genome assemblies.

PubMed

Howe, Kerstin; Wood, Jonathan M D

2015-01-01

Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction digest maps. Because it is not subject to cloning, amplification, hybridisation or sequencing bias, it is ideally suited to the improvement of fragmented genome assemblies that can no longer be improved by classical methods. In addition, its low cost and rapid turnaround make it equally useful during the scaffolding process of de novo assembly from high throughput sequencing reads. We describe how optical mapping has been used in practice to produce high quality vertebrate genome assemblies. In particular, we detail the efforts undertaken by the Genome Reference Consortium (GRC), which maintains the reference genomes for human, mouse, zebrafish and chicken, and uses different optical mapping platforms for genome curation.

Tunable optical metamaterial based on liquid crystal-gold nanosphere composite.

PubMed

Pratibha, R; Park, K; Smalyukh, I I; Park, W

2009-10-26

Effect of the surrounding anisotropic liquid crystal medium on the surface plasmon resonance (SPR) exhibited by concentrated suspensions of gold nanospheres has been investigated experimentally and compared with the Mie scattering theory. The observed polarization-sensitive SPR and the red-shift in the SPR wavelength with increasing concentration of the gold nanospheres in the liquid crystal matrix have been explained using calculations based on the Maxwell Garnet effective medium theory. Agglomeration of the gold nanospheres that could also lead to such a red-shift has been ruled out using Atomic force microscopy study of thin nanoparticle-doped smectic films obtained on solid substrates. Our study demonstrates feasibility of obtaining tunable optical bulk metamaterials based on smectic liquid crystal - nanoparticle composites.

Continuous-wave ultraviolet generation at 320 nm by intracavity frequency doubling of red-emitting Praseodymium lasers

NASA Astrophysics Data System (ADS)

Richter, A.; Pavel, N.; Heumann, E.; Huber, G.; Parisi, D.; Toncelli, A.; Tonelli, M.; Diening, A.; Seelert, W.

2006-04-01

We describe a new approach for the generation of coherent ultraviolet radiation. Continuous-wave ultraviolet light at 320 nm has been obtained by intracavity frequency doubling of red-emitting Praseodymium lasers. Lasing at the 640-nm fundamental wavelength in Pr:LiYF4 and Pr:BaY2F8 was realized by employing an optically pumped semiconductor laser at 480 nm as pump source.Using LiB3O5 as nonlinear medium, ~19 mW of ultraviolet radiation with ~9% optical efficiency with respect to absorbed power was reached for both laser crystals; the visible-to-ultraviolet conversion efficiency was 26% and 35% for Pr:LiYF4 and Pr:BaY2F8, respectively.

Optical Experiments Using Mini-Torches with Red, Green and Blue Light Emitting Diodes

ERIC Educational Resources Information Center

Kamata, Masahiro; Matsunaga, Ai

2007-01-01

We have developed two kinds of optical experiments: color mixture and fluorescence, using mini-torches with light emitting diodes (LEDs) that emit three primary colors. Since the tools used in the experiments are simple and inexpensive, students can easily retry and develop the experiments by themselves. As well as giving an introduction to basic…

New biodiagnostics based on optical tweezers: typing red blood cells, and identification of drug resistant bacteria

NASA Astrophysics Data System (ADS)

Chen, Jia-Wen; Lin, Chuen-Fu; Wang, Shyang-Guang; Lee, Yi-Chieh; Chiang, Chung-Han; Huang, Min-Hui; Lee, Yi-Hsiung; Vitrant, Guy; Pan, Ming-Jeng; Lee, Horng-Mo; Liu, Yi-Jui; Baldeck, Patrice L.; Lin, Chih-Lang

2013-09-01

Measurements of optical tweezers forces on biological micro-objects can be used to develop innovative biodiagnostics methods. In the first part of this report, we present a new sensitive method to determine A, B, D types of red blood cells. Target antibodies are coated on glass surfaces. Optical forces needed to pull away RBC from the glass surface increase when RBC antigens interact with their corresponding antibodies. In this work, measurements of stripping optical forces are used to distinguish the major RBC types: group O Rh(+), group A Rh(+) and group B Rh(+). The sensitivity of the method is found to be at least 16-folds higher than the conventional agglutination method. In the second part of this report, we present an original way to measure in real time the wall thickness of bacteria that is one of the most important diagnostic parameters of bacteria drug resistance in hospital diagnostics. The optical tweezers force on a shell bacterium is proportional to its wall thickness. Experimentally, we determine the optical tweezers force applied on each bacteria family by measuring their escape velocity. Then, the wall thickness of shell bacteria can be obtained after calibrating with known bacteria parameters. The method has been successfully applied to indentify, from blind tests, Methicillinresistant Staphylococcus aureus (MRSA), including VSSA (NCTC 10442), VISA (Mu 50), and heto-VISA (Mu 3)

De Novo Transcriptome Sequencing Analysis of cDNA Library and Large-Scale Unigene Assembly in Japanese Red Pine (Pinus densiflora)

PubMed Central

Liu, Le; Zhang, Shijie; Lian, Chunlan

2015-01-01

Japanese red pine (Pinus densiflora) is extensively cultivated in Japan, Korea, China, and Russia and is harvested for timber, pulpwood, garden, and paper markets. However, genetic information and molecular markers were very scarce for this species. In this study, over 51 million sequencing clean reads from P. densiflora mRNA were produced using Illumina paired-end sequencing technology. It yielded 83,913 unigenes with a mean length of 751 bp, of which 54,530 (64.98%) unigenes showed similarity to sequences in the NCBI database. Among which the best matches in the NCBI Nr database were Picea sitchensis (41.60%), Amborella trichopoda (9.83%), and Pinus taeda (4.15%). A total of 1953 putative microsatellites were identified in 1784 unigenes using MISA (MicroSAtellite) software, of which the tri-nucleotide repeats were most abundant (50.18%) and 629 EST-SSR (expressed sequence tag- simple sequence repeats) primer pairs were successfully designed. Among 20 EST-SSR primer pairs randomly chosen, 17 markers yielded amplification products of the expected size in P. densiflora. Our results will provide a valuable resource for gene-function analysis, germplasm identification, molecular marker-assisted breeding and resistance-related gene(s) mapping for pine for P. densiflora. PMID:26690126

Life style and biochemical adaptation in Antarctic fishes

NASA Astrophysics Data System (ADS)

di Prisco, Guido

2000-12-01

Respiration and metabolism are under investigation in Antarctic fish, in an effort to understand the interplay between ecology and biochemical and physiological processes. Fish of the dominant suborder Notothenioidei are red-blooded, except Channichthyidae (the most phyletically derived family), whose genomes retain transcriptionally inactive DNA sequences closely related to the α-globin gene of red-blooded notothenioids and have lost the β-globin locus. Our structure/function studies on 38 of the 80 red-blooded species are aimed at correlating sequence, multiplicity and oxygen binding with ecological constraints and at obtaining phylogenetic information on evolution. For comparative purposes, this work has been extended to non-Antarctic notothenioids. All sluggish bottom dwellers have a single major hemoglobin (Hb) and often a minor, functionally similar one. Three species of the family Nototheniidae have different life styles. They have uniquely specialised oxygen-transport systems, adjusted to the mode of life of each species. Artedidraconidae have a single Hb, lacking oxygen-binding cooperativity, similar to the ancestral hemoproteins of primitive organisms. The amino acid sequences are currently used in the molecular modelling approach. The study of several enzymes with key roles in metabolism (e.g. glucose-6-phosphate dehydrogenase, L-glutamate dehydrogenase, phosphorylase b, carbonic anhydrase) indicate that some aspects of the molecular structure (e.g. molecular mass, number of subunits, amino acid sequence, temperature of irreversible heat inactivation) have been conserved during development of cold adaptation. However, high catalytic efficiency, possibly due to subtle molecular changes, is observed at low temperature.

Compact high-power red-green-blue laser light source generation from a single lithium tantalate with cascaded domain modulation.

PubMed

Xu, P; Zhao, L N; Lv, X J; Lu, J; Yuan, Y; Zhao, G; Zhu, S N

2009-06-08

1W quasi-white-light source has been generated from a single lithium tantalate with cascaded domain modulation. The quasi-white-light is combined by proper proportion of the red, green and blue laser light. The red and the blue result from a compact self-sum frequency optical parametric oscillation when pumped by a single green laser. The efficiency of quasi-white-light from the green pump reaches 27%. This compact design can be employed not only as a stable and powerful RGB light source but also an effective blue laser generator.

The High AV Quasar Survey: Reddened Quasi-Stellar Objects Selected from Optical/Near-Infrared Photometry—II

NASA Astrophysics Data System (ADS)

Krogager, J.-K.; Geier, S.; Fynbo, J. P. U.; Venemans, B. P.; Ledoux, C.; Møller, P.; Noterdaeme, P.; Vestergaard, M.; Kangas, T.; Pursimo, T.; Saturni, F. G.; Smirnova, O.

2015-03-01

Quasi-stellar objects (QSOs) whose spectral energy distributions (SEDs) are reddened by dust either in their host galaxies or in intervening absorber galaxies are to a large degree missed by optical color selection criteria like the ones used by the Sloan Digital Sky Survey (SDSS). To overcome this bias against red QSOs, we employ a combined optical and near-infrared (near-IR) color selection. In this paper, we present a spectroscopic follow-up campaign of a sample of red candidate QSOs which were selected from the SDSS and the UKIRT Infrared Deep Sky Survey (UKIDSS). The spectroscopic data and SDSS/UKIDSS photometry are supplemented by mid-infrared photometry from the Wide-field Infrared Survey Explorer. In our sample of 159 candidates, 154 (97%) are confirmed to be QSOs. We use a statistical algorithm to identify sightlines with plausible intervening absorption systems and identify nine such cases assuming dust in the absorber similar to Large Magellanic Cloud sightlines. We find absorption systems toward 30 QSOs, 2 of which are consistent with the best-fit absorber redshift from the statistical modeling. Furthermore, we observe a broad range in SED properties of the QSOs as probed by the rest-frame 2 μm flux. We find QSOs with a strong excess as well as QSOs with a large deficit at rest-frame 2 μm relative to a QSO template. Potential solutions to these discrepancies are discussed. Overall, our study demonstrates the high efficiency of the optical/near-IR selection of red QSOs.

The physical properties of galaxies with unusually red mid-infrared colours

NASA Astrophysics Data System (ADS)

Kauffmann, Guinevere

2018-02-01

The goal of this paper is to investigate the physical nature of galaxies in the redshift range 0.02 < z < 0.15 that have strong excess emission at mid-infrared wavelengths and to determine whether they host a population of accreting black holes that cannot be identified using optical emission lines. We show that at fixed stellar mass M* and Dn(4000), the distribution of [3.4]-[4.6] μm (Wide-field Infrared Survey Explorer, W1 - W2 band) colours is sharply peaked, with a long tail to much redder W1 - W2 colours. We introduce a procedure to pull out the red outlier population based on a combination of three stellar population diagnostics. When compared with optically selected active galactic nucleus (AGN), red outliers are more likely to be found in massive galaxies, and they tend to have lower stellar mass densities, younger stellar ages and higher dust content than optically selected AGN hosts. They are twice as likely to be detected at radio wavelengths. We examine W1 - W2 colour profiles for a subset of the nearest, reddest outliers and find that most are not centrally peaked, indicating that the hot dust emission is spread throughout the galaxy. We find that radio luminosity is the quantity that is most predictive of a redder central W1 - W2 colour. Radio-loud galaxies with centrally concentrated hot dust emission are almost always morphologically disturbed, with compact, unresolved emission at 1.4 GHz. The 80 per cent of such systems are identifiable as AGN using optical emission line diagnostics.

LED backlight system with fiber-optic red, green, blue to white color combiner

NASA Astrophysics Data System (ADS)

Kim, Hye R.; Jeong, Yunsong; Lee, Jhang-Woo; Oh, Kyunghwan

2006-09-01

As an application in the backlight system of small LCD display, we realized a pure white light source by mixing red, green, blue (RGB) lights using a 3 X 3 Hard Plastic Cladding Fiber (HPCF) coupler. We also proposed the 0.44 inch LED backlight system with these fiber-optic pure white sources and characterized its illumination characteristics. Using optimized fusion-tapering technique, we fabricated HPCF coupler which combines three input lights over the circularly formed waist. HPCF has the core diameter of 200 μm and clad diameter of 230 μm. The fabricated 3 X 3 HPCF coupler has the perfect uniformity of about 0.3 dB, low insertion loss of 5.5 dB, and low excess loss of 0.8 dB, which shows excellent uniform power splitting ratio. In order to improve the transmission performance, The RGB chip LEDs were butt-coupled directly to the ferruled input ports of the coupler and packaged by TO46-can type. In the produced white color by HPCF coupler, the photometric brightness at the circular endface of outputs of HPCF coupler was in a rage of 10062 ~ 10094 cd/m2. The fiber optic white color combiner provides tunable white sources excluding heat source and having thickness of 200 μm. We also proposed a 0.44 inch LED backlight system with these fiber-optic pure white sources. With the proposed device, we obtain the improved uniformity in luminance distribution and wide color gamut by using the white light mixing red, green and blue lights.

Image correlation method for DNA sequence alignment.

PubMed

Curilem Saldías, Millaray; Villarroel Sassarini, Felipe; Muñoz Poblete, Carlos; Vargas Vásquez, Asticio; Maureira Butler, Iván

2012-01-01

The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.

Quantum size and magnesium composition effects on the optical absorption in the MgxZn(1-x)O/ZnO quantum well

NASA Astrophysics Data System (ADS)

Dakhlaoui, Hassen ben Bechir; Mouna, Nefzi

2018-02-01

In this work, we investigated the effects of polarizations and structural parameters on the optical absorption coefficient (OAC) and the intersubband transition between the three lowest energy levels E1,E2 , and E3 in the MgxZn(1-x)O/ZnO single quantum well. The energy of the electron in each level and its respective wavefunction are calculated by the numerical solution of Schrödinger and Poisson equations self-consistently using an effective mass approximation. Our findings exhibit that the intersubband transitions, ΔE12 and ΔE13 , can be altered and controlled by varying the quantum well width and the magnesium composition, x. Moreover, our results suggest that the optical absorption coefficients, α12 and α13 , can be modulated principally by adjusting the quantum well width, especially the optical absorption coefficient (α12), which presents a red shift by raising the quantum well thickness. Contrary to α12 , the optical absorption coefficient, α13 , can present either a red or a blue shift by increasing the quantum well width. The process responsible for this behavior, which can be suitable for optoelectronic device applications, is discussed here in detail.

Broadband Fluorescence Enhancement with Self-Assembled Silver Nanoparticle Optical Antennas.

PubMed

Vietz, Carolin; Kaminska, Izabela; Sanz Paz, Maria; Tinnefeld, Philip; Acuna, Guillermo P

2017-05-23

Plasmonic structures are known to affect the fluorescence properties of dyes placed in close proximity. This effect has been exploited in combination with single-molecule techniques for several applications in the field of biosensing. Among these plasmonic structures, top-down zero-mode waveguides stand out due to their broadband capabilities. In contrast, optical antennas based on gold nanostructures exhibit fluorescence enhancement on a narrow fraction of the visible spectrum typically restricted to the red to near-infrared region. In this contribution, we exploit the DNA origami technique to self-assemble optical antennas based on large (80 nm) silver nanoparticles. We have studied the performance of these antennas with far- and near-field simulations and characterized them experimentally with single-molecule fluorescence measurements. We demonstrate that silver-based optical antennas can yield a fluorescence enhancement of more than 2 orders of magnitude throughout the visible spectral range for high intrinsic quantum yield dyes. Additionally, a comparison between the performance of gold and silver-based antennas is included. The results indicate that silver-based antennas strongly outperform their gold counterparts in the blue and green ranges and exhibit marginal differences in the red range. These characteristics render silver-based optical antennas ready for applications involving several fluorescently labeled species across the visible spectrum.

In vivo imaging of mammalian cochlear blood flow using fluorescence microendoscopy.

PubMed

Monfared, Ashkan; Blevins, Nikolas H; Cheung, Eunice L M; Jung, Juergen C; Popelka, Gerald; Schnitzer, Mark J

2006-02-01

We sought to develop techniques for visualizing cochlear blood flow in live mammalian subjects using fluorescence microendoscopy. Inner ear microcirculation appears to be intimately involved in cochlear function. Blood velocity measurements suggest that intense sounds can alter cochlear blood flow. Disruption of cochlear blood flow may be a significant cause of hearing impairment, including sudden sensorineural hearing loss. However, inability to image cochlear blood flow in a nondestructive manner has limited investigation of the role of inner ear microcirculation in hearing function. Present techniques for imaging cochlear microcirculation using intravital light microscopy involve extensive perturbations to cochlear structure, precluding application in human patients. The few previous endoscopy studies of the cochlea have suffered from optical resolution insufficient for visualizing cochlear microvasculature. Fluorescence microendoscopy is an emerging minimally invasive imaging modality that provides micron-scale resolution in tissues inaccessible to light microscopy. In this article, we describe the use of fluorescence microendoscopy in live guinea pigs to image capillary blood flow and movements of individual red blood cells within the basal turn of the cochlea. We anesthetized eight adult guinea pigs and accessed the inner ear through the mastoid bulla. After intravenous injection of fluorescein dye, we made a limited cochleostomy and introduced a compound doublet gradient refractive index endoscope probe 1 mm in diameter into the inner ear. We then imaged cochlear blood flow within individual vessels in an epifluorescence configuration using one-photon fluorescence microendoscopy. We observed single red blood cells passing through individual capillaries in several cochlear structures, including the round window membrane, spiral ligament, osseous spiral lamina, and basilar membrane. Blood flow velocities within inner ear capillaries varied widely, with observed speeds reaching up to approximately 500 microm/s. Fluorescence microendoscopy permits visualization of cochlear microcirculation with micron-scale optical resolution and determination of blood flow velocities through analysis of video sequences.

Optical Alignment and Diffraction Analysis for AIRES: An Airborne Infrared Echelle Spectrometer

NASA Technical Reports Server (NTRS)

Haas, Michael R.; Fonda, Mark (Technical Monitor)

2002-01-01

The optical design is presented for a long-slit grating spectrometer known as AIRES (Airborne InfraRed Echelle Spectrometer). The instrument employs two gratings in series: a small order sorter and a large steeply blazed echelle. The optical path includes four pupil and four field stops, including two narrow slits. A detailed diffraction analysis is performed using GLAD by Applied Optics Research to evaluate critical trade-offs between optical throughput, spectral resolution, and system weight and volume. The effects of slit width, slit length, oversizing the second slit relative to the first, on- vs off-axis throughput, and clipping at the pupil stops and other optical elements are discussed.

Joint electrical engineering/physics course sequence for optics fundamentals and design

NASA Astrophysics Data System (ADS)

Magnusson, Robert; Maldonado, Theresa A.; Black, Truman D.

2000-06-01

Optics is a key technology in a broad range of engineering and science applications of high national priority. Engineers and scientists with a sound background in this field are needed to preserve technical leadership and to establish new directions of research and development. To meet this educational need, a joint Electrical Engineering/Physics optics course sequence was created as PHYS 3445 Fundamentals of Optics and EE 4444 Optical Systems Design, both with a laboratory component. The objectives are to educate EE and Physics undergraduate students in the fundamentals of optics; in interdisciplinary problem solving; in design and analysis; in handling optical components; and in skills such as communications and team cooperation. Written technical reports in professional format are required, formal presentations are given, and participation in paper design contests is encouraged.

Exobasidium maculosum, a new species causing leaf and fruit spots on blueberry in the southeastern USA and its relationship with other Exobasidium spp. parasitic to blueberry and cranberry.

PubMed

Brewer, Marin Talbot; Turner, Ashley N; Brannen, Phillip M; Cline, William O; Richardson, Elizabeth A

2014-01-01

Exobasidium leaf and fruit spot of blueberry (Vaccinium section Cyanococcus) is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA. To determine whether this disease is caused by a new species of Exobasidium, we studied the morphology and phylogenetic relationship of the causal fungus compared with other members of the genus, including the type species E. vaccinii and other species that parasitize blueberry and cranberry (V. macrocarpon). Both scanning electron microscopy and light microscopy were used for morphological characterization. For phylogenetic analyses, we sequenced the large subunit of the rDNA (LSU) from 10 isolates collected from leaf or fruit spots of rabbiteye blueberry (V. virgatum), highbush blueberry (V. corymbosum) and southern highbush blueberry (Vaccinium interspecific hybrid) from Georgia and North Carolina and six isolates from leaf spots of lowbush blueberry (V. angustifolium) from Maine and Nova Scotia, Canada. LSU was sequenced from isolates causing red leaf disease of lowbush blueberry and red leaf spot (E. rostrupii) and red shoot (E. perenne) of cranberry. In addition, LSU sequences from GenBank, including sequences with high similarity to the emerging parasite and from Exobasidium spp. parasitizing other Vaccinium spp. and related hosts, were obtained. All sequences were aligned and subjected to phylogenetic analyses. Results indicated that the emerging parasite in the southeastern USA differs morphologically and phylogenetically from other described species and is described herein as Exobasidium maculosum. Within the southeastern USA, clustering based on host species, host tissue type (leaf or fruit) or geographic region was not detected; however, leaf spot isolates from lowbush blueberry were genetically different and likely represent a unique species. © 2014 by The Mycological Society of America.

Coherent direct sequence optical code multiple access encoding-decoding efficiency versus wavelength detuning.

PubMed

Pastor, D; Amaya, W; García-Olcina, R; Sales, S

2007-07-01

We present a simple theoretical model of and the experimental verification for vanishing of the autocorrelation peak due to wavelength detuning on the coding-decoding process of coherent direct sequence optical code multiple access systems based on a superstructured fiber Bragg grating. Moreover, the detuning vanishing effect has been explored to take advantage of this effect and to provide an additional degree of multiplexing and/or optical code tuning.

Radar and photometric measurements of an intense type A red aurora

NASA Technical Reports Server (NTRS)

Robinson, R. M.; Mende, S. B.; Vondrak, R. R.; Kozyra, J. U.; Nagy, A. F.

1985-01-01

On the evening of March 5, 1981, an intense, type A red aurora appeared over southern Alaska. Radar and photometric measurements were made of the aurora from the Chatanika radar site. The line of sight intensity of the 630.0-nm emissions exceeded 150 kR and was accompanied by enhanced emissions at 486.1 and 427.8 nm. The Chatanika radar measured electron densities of 10 to the 6th per cu cm and electron temperatures of 6000 K at an altitude of 400 km and an invariant latitude of 59 deg in association with the aurora. Comparison of optical and radar measurements indicated that the 630.0-nm emissions were produced to a large degree by thermal excitation of O(1D) in the region of high electron temperatures and densities. Model calculations indicate that the observed density and temperature enhancements and the related optical emissions were the results of a relatively short duration (5-10 min) pulse of precipitating, low-energy (about 30 eV) electrons. Whereas conventional stable auroral red arcs are associated with a gradual decrease in ring current energy density during the recovery phase of a magnetic storm, the type A red aurora may be produced by impulsive ring current energy loss during the main phase.

Optical Pattern Formation in Cold Atoms: Explaining the Red-Blue Asymmetry

NASA Astrophysics Data System (ADS)

Schmittberger, Bonnie; Gauthier, Daniel

2013-05-01

The study of pattern formation in atomic systems has provided new insight into fundamental many-body physics and low-light-level nonlinear optics. Pattern formation in cold atoms in particular is of great interest in condensed matter physics and quantum information science because atoms undergo self-organization at ultralow input powers. We recently reported the first observation of pattern formation in cold atoms but found that our results were not accurately described by any existing theoretical model of pattern formation. Previous models describing pattern formation in cold atoms predict that pattern formation should occur using both red and blue-detuned pump beams, favoring a lower threshold for blue detunings. This disagrees with our recent work, in which we only observed pattern formation with red-detuned pump beams. Previous models also assume a two-level atom, which cannot account for the cooling processes that arise when beams counterpropagate through a cold atomic vapor. We describe a new model for pattern formation that accounts for Sisyphus cooling in multi-level atoms, which gives rise to a new nonlinearity via spatial organization of the atoms. This spatial organization causes a sharp red-blue detuning asymmetry, which agrees well with our experimental observations. We gratefully acknowledge the financial support of the NSF through Grant #PHY-1206040.

Effect of red clay on diesel bioremediation and soil bacterial community.

PubMed

Jung, Jaejoon; Choi, Sungjong; Hong, Hyerim; Sung, Jung-Suk; Park, Woojun

2014-08-01

Red clay is a type of soil, the red color of which results from the presence of iron oxide. It is considered an eco-friendly material, with many industrial, cosmetic, and architectural uses. A patented method was applied to red clay in order to change its chemical composition and mineral bioavailability. The resulting product was designated processed red clay. This study evaluates the novel use of red clay and processed red clay as biostimulation agents in diesel-contaminated soils. Diesel biodegradation was enhanced in the presence of red clay and processed red clay by 4.9- and 6.7-fold, respectively, and the number of culturable bacterial cells was correlated with the amount of diesel biodegradation. The growth of Acinetobacter oleivorans DR1, Pseudomonas putida KT2440, and Cupriavidus necator was promoted by both types of red clays. Culture-independent community analysis determined via barcoded pyrosequencing indicated that Nocardioidaceae, Xanthomonadaceae, Pseudomonadaceae, and Caulobacteraceae were enriched by diesel contamination. Bacterial strain isolation from naphthalene- and liquid paraffin-amended media was affiliated with enriched taxa based on 16S rRNA gene sequence identity. We suggest that the biostimulating mechanism of red clay and processed red clay is able to support bacterial growth without apparent selection for specific bacterial species.

Controlled core removal from a D-shaped optical fiber.

PubMed

Markos, Douglas J; Ipson, Benjamin L; Smith, Kevin H; Schultz, Stephen M; Selfridge, Richard H; Monte, Thomas D; Dyott, Richard B; Miller, Gregory

2003-12-20

The partial removal of a section of the core from a continuous D-shaped optical fiber is presented. In the core removal process, selective chemical etching is used with hydrofluoric (HF) acid. A 25% HF acid solution removes the cladding material above the core, and a 5% HF acid solution removes the core. A red laser with a wavelength of 670 nm is transmitted through the optical fiber during the etching. The power transmitted through the optical fiber is correlated to the etch depth by scanning electron microscope imaging. The developed process provides a repeatable method to produce an optical fiber with a specific etch depth.

Analysis of Remote Sensing Data Reveals the Correlation of Anomalies between Aerosol Optical Depth and Chlorophyll-a Concentrations in the Red Sea Area

NASA Astrophysics Data System (ADS)

Coria, J.; Bonilla, J., III; Li, W.; El-Askary, H. M.; Qurban, M.; Garay, M. J.; Kalashnikova, O. V.

2017-12-01

The Red Sea has one of the highest salinities and one of the most diverse ecosystems in the world. We wanted to investigate how chlorophyll-a contributes to this diverse ecosystem. From 2002 to 2015, we observed an increase in aerosol optical depth (AOD) levels which we believed contributed to an increase in chlorophyll-a concentration levels. Focusing on the Red Sea we used the Moderate Resolution Imaging Spectroradiometer (MODIS) on board the Terra and Aqua platforms in order to acquire the data necessary for our research. After gathering the monthly data for the chlorophyll-a concentration and AOD for this period we normalized the data in order to find correlations between the two parameters. We found that there was a continuous increase in AOD from 2002 to 2015. Inversely we found that there was an overall decrease in chlorophyll-a concentration during this same time period. However, there was a correlation between AOD anomalies and chlorophyll-a anomalies that did not follow the decreasing trend of chlorophyll-a. These findings exemplified a two-month lag between the AOD anomalies and chlorophyll-a concentration anomalies. This shows that the increase in AOD has a significant impact on the chlorophyll-a conentration anomalies which in turn contributes to the overall greenness of the Red Sea. This is significant because there are many cities surrounding the Red Sea that depend on this diverse ecosystem as a stable food source.

The X-ray luminous galaxy cluster XMMU J1007.4+1237 at z = 1.56. The dawn of starburst activity in cluster cores

NASA Astrophysics Data System (ADS)

Fassbender, R.; Nastasi, A.; Böhringer, H.; Šuhada, R.; Santos, J. S.; Rosati, P.; Pierini, D.; Mühlegger, M.; Quintana, H.; Schwope, A. D.; Lamer, G.; de Hoon, A.; Kohnert, J.; Pratt, G. W.; Mohr, J. J.

2011-03-01

Context. Observational galaxy cluster studies at z > 1.5 probe the formation of the first massive M > 1014 M⊙ dark matter halos, the early thermal history of the hot ICM, and the emergence of the red-sequence population of quenched early-type galaxies. Aims: We present first results for the newly discovered X-ray luminous galaxy cluster XMMU J1007.4+1237 at z = 1.555, detected and confirmed by the XMM-Newton Distant Cluster Project (XDCP) survey. Methods: We selected the system as a serendipitous weak extended X-ray source in XMM-Newton archival data and followed it up with two-band near-infrared imaging and deep optical spectroscopy. Results: We can establish XMMU J1007.4+1237 as a spectroscopically confirmed, massive,bona fide galaxy cluster with a bolometric X-ray luminosity of Lbol_X,500≃(2.1 ± 0.4)× 10^{44} erg/s, a red galaxy population centered on the X-ray emission, and a central radio-loud brightest cluster galaxy. However, we see evidence for the first time that the massive end of the galaxy population and the cluster red-sequence are not yet fully in place. In particular, we find ongoing starburst activity for the third ranked galaxy close to the center and another slightly fainter object. Conclusions: At a lookback time of 9.4 Gyr, the cluster galaxy population appears to be caught in an important evolutionary phase, prior to full star-formation quenching and mass assembly in the core region. X-ray selection techniques are an efficient means of identifying and probing the most distant clusters without any prior assumptions about their galaxy content. Based on observations under programme ID 081.A-0312 collected at the European Organisation for Astronomical Research in the Southern Hemisphere, Chile, and observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC).Figure 2 and Tables 1 and 2 are only available in electronic form at http://www.aanda.org

Systematic control of optical features in aluminosilicate glass waveguides using direct femtosecond laser writing

NASA Astrophysics Data System (ADS)

Babu, B. Hari; Niu, Mengsi; Yang, Xiaoyu; Wang, Yanbo; Feng, Lin; Qin, Wei; Hao, Xiao-Tao

2017-10-01

Low loss optical waveguides inside aluminosilicate glasses have been successfully fabricated using direct femtosecond laser writing. To establish the influence of pulse energy and host variations on the optical waveguides have been tentatively explored and systematically studied with the help of different spectroscopic techniques. Isochronal annealing treatment effectively reduces the insertion losses to 1.01 ± 0.28 dB at 632.8 nm. A red shift of the Raman band has been observed with increasing Al2O3 content due to the bond angle variations. The point defects such as non-bridging oxygen hole centers have been corroborated by the photoluminescence studies and significant red-shift has also been documented with increasing Al2O3 content. In addition, there is no NBOHC defects perceived after isochronal annealing treatment inside the glass waveguides. Our results envisage that the present glass waveguides should be promising and potential for applications in passive waveguides and integrated photonic devices.

Far-red light photoactivatable near-infrared fluorescent proteins engineered from a bacterial phytochrome.

PubMed

Piatkevich, Kiryl D; Subach, Fedor V; Verkhusha, Vladislav V

2013-01-01

The ability to modulate the fluorescence of optical probes can be used to enhance signal-to-noise ratios for imaging within highly autofluorescent environments, such as intact tissues and living organisms. Here, we report two bacteriophytochrome-based photoactivatable near-infrared fluorescent proteins, named PAiRFP1 and PAiRFP2. PAiRFPs utilize haem-derived biliverdin, ubiquitous in mammalian tissues, as the chromophore. Initially weakly fluorescent PAiRFPs undergo photoconversion into a highly fluorescent state with excitation/emission at 690/717 nm following a brief irradiation with far-red light. After photoactivation, PAiRFPs slowly revert back to initial state, enabling multiple photoactivation-relaxation cycles. Low-temperature optical spectroscopy reveals several intermediates involved in PAiRFP photocycles, which all differ from that of the bacteriophytochrome precursor. PAiRFPs can be photoactivated in a spatially selective manner in mouse tissues, and optical modulation of their fluorescence allows for substantial contrast enhancement, making PAiRFPs advantageous over permanently fluorescent probes for in vivo imaging conditions of high autofluorescence and low signal levels.

Optical properties modification induced by laser radiation in noble-metal-doped glasses

NASA Astrophysics Data System (ADS)

Nedyalkov, N.; Stankova, N. E.; Koleva, M. E.; Nikov, R.; Atanasov, P.; Grozeva, M.; Iordanova, E.; Yankov, G.; Aleksandrov, L.; Iordanova, R.; Karashanova, D.

2018-03-01

We present results on laser-induced color changes in gold- and silver-doped glass. The doped borosilicate glass was prepared by conventional melt quenching. The study was focused on the change of the optical properties after irradiation of the glass by femtosecond laser pulses. Under certain conditions, the laser radiation induces defects associated with formation of color centers in the material. We studied this process in a broad range of laser radiation wavelengths – from UV to IR, and observed changes in the color of the irradiated areas after annealing of the processed glass samples, the color being red for the gold-doped glass red and yellow for the silver-doped glass. The structural and morphological analyses performed indicated that this effect is related to formation of metal nanoparticles inside the material. The results obtained show that femtosecond laser processing of noble-metal-doped glasses can be used for fabrication of 3D-nanoparticles systems in transparent materials with application as novel optical components.

Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae.

PubMed

Boo, Ga Hun; Hughey, Jeffery R; Miller, Kathy Ann; Boo, Sung Min

2016-10-14

DNA sequences from type specimens provide independent, objective characters that enhance the value of type specimens and permit the correct application of species names to phylogenetic clades and specimens. We provide mitochondrial genomes (mitogenomes) from archival type specimens of ten species in agar-producing red algal genera Gelidium and Pterocladiella. The genomes contain 43-44 genes, ranging in size from 24,910 to 24,970 bp with highly conserved gene synteny. Low Ka/Ks ratios of apocytochrome b and cytochrome oxidase genes support their utility as markers. Phylogenies of mitogenomes and cox1+rbcL sequences clarified classification at the genus and species levels. Three species formerly in Gelidium and Pterocladia are transferred to Pterocladiella: P. media comb. nov., P. musciformis comb. nov., and P. luxurians comb. and stat. nov. Gelidium sinicola is merged with G. coulteri because they share identical cox1 and rbcL sequences. We describe a new species, Gelidium millariana sp. nov., previously identified as G. isabelae from Australia. We demonstrate that mitogenomes from type specimens provide a new tool for typifying species in the Gelidiales and that there is an urgent need for analyzing mitogenomes from type specimens of red algae and other morphologically simple organisms for insight into their nomenclature, taxonomy and evolution.

Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae

PubMed Central

Boo, Ga Hun; Hughey, Jeffery R.; Miller, Kathy Ann; Boo, Sung Min

2016-01-01

DNA sequences from type specimens provide independent, objective characters that enhance the value of type specimens and permit the correct application of species names to phylogenetic clades and specimens. We provide mitochondrial genomes (mitogenomes) from archival type specimens of ten species in agar-producing red algal genera Gelidium and Pterocladiella. The genomes contain 43–44 genes, ranging in size from 24,910 to 24,970 bp with highly conserved gene synteny. Low Ka/Ks ratios of apocytochrome b and cytochrome oxidase genes support their utility as markers. Phylogenies of mitogenomes and cox1+rbcL sequences clarified classification at the genus and species levels. Three species formerly in Gelidium and Pterocladia are transferred to Pterocladiella: P. media comb. nov., P. musciformis comb. nov., and P. luxurians comb. and stat. nov. Gelidium sinicola is merged with G. coulteri because they share identical cox1 and rbcL sequences. We describe a new species, Gelidium millariana sp. nov., previously identified as G. isabelae from Australia. We demonstrate that mitogenomes from type specimens provide a new tool for typifying species in the Gelidiales and that there is an urgent need for analyzing mitogenomes from type specimens of red algae and other morphologically simple organisms for insight into their nomenclature, taxonomy and evolution. PMID:27739454

Acne at The Bottom Of The Main Sequence

NASA Astrophysics Data System (ADS)

Barnes, John; Haswell, C.; Jenkins, J.; Jeffers, S.; Jones, H. R. A.; Lohr, M.; Pavlenko, Y.

2016-08-01

Starspots are an important manifestation of stellar activity and yet their distribution patterns on the lowest mass stars is not well known. Time series spectra of fully convective M dwarfs taken in the red-optical with UVES reveal numerous line profile distortions which are interpreted as starspots. We derive Doppler images for four M4.5V - M9V stars and find that contrast ratios corresponding to photosphere-spot temperature differences of only 200-300 K are sufficient to model the timeseries spectra. Although more starspot structure is found at high latitudes, spots are reconstructed at a range of phases and latitudes with mean spot filling factors of only a few per cent. The occurrence of low-contrast spots at predominantly high latitudes is in general likely to be responsible for the low amplitude photometric variability seen in late-M dwarfs. The recovered starspot patterns are used to assess their effect on precision radial velocity surveys aimed at detecting planets around this population of stars.

Chromosomal Mapping of Canine-Derived BAC Clones to the Red Fox and American Mink Genomes

PubMed Central

Vorobieva, Nadegda V.; Beklemisheva, Violetta R.; Johnson, Jennifer L.; Temnykh, Svetlana V.; Yudkin, Dmitry V.; Trut, Lyudmila N.; Andre, Catherine; Galibert, Francis; Aguirre, Gustavo D.; Acland, Gregory M.; Graphodatsky, Alexander S.

2009-01-01

High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene–containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations. PMID:19546120

Chromosomal mapping of canine-derived BAC clones to the red fox and American mink genomes.

PubMed

Kukekova, Anna V; Vorobieva, Nadegda V; Beklemisheva, Violetta R; Johnson, Jennifer L; Temnykh, Svetlana V; Yudkin, Dmitry V; Trut, Lyudmila N; Andre, Catherine; Galibert, Francis; Aguirre, Gustavo D; Acland, Gregory M; Graphodatsky, Alexander S

2009-01-01

High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene-containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations.

Coinfection of Ugandan Red Colobus (Procolobus [Piliocolobus] rufomitratus tephrosceles) with Novel, Divergent Delta-, Lenti-, and Spumaretroviruses ▿

PubMed Central

Goldberg, Tony L.; Sintasath, David M.; Chapman, Colin A.; Cameron, Kenneth M.; Karesh, William B.; Tang, Shaohua; Wolfe, Nathan D.; Rwego, Innocent B.; Ting, Nelson; Switzer, William M.

2009-01-01

Nonhuman primates host a plethora of potentially zoonotic microbes, with simian retroviruses receiving heightened attention due to their roles in the origins of human immunodeficiency viruses type 1 (HIV-1) and HIV-2. However, incomplete taxonomic and geographic sampling of potential hosts, especially the African colobines, has left the full range of primate retrovirus diversity unexplored. Blood samples collected from 31 wild-living red colobus monkeys (Procolobus [Piliocolobus] rufomitratus tephrosceles) from Kibale National Park, Uganda, were tested for antibodies to simian immunodeficiency virus (SIV), simian T-cell lymphotrophic virus (STLV), and simian foamy virus (SFV) and for nucleic acids of these same viruses using genus-specific PCRs. Of 31 red colobus tested, 22.6% were seroreactive to SIV, 6.4% were seroreactive to STLV, and 97% were seroreactive to SFV. Phylogenetic analyses of SIV polymerase (pol), STLV tax and long terminal repeat (LTR), and SFV pol and LTR sequences revealed unique SIV and SFV strains and a novel STLV lineage, each divergent from corresponding retroviral lineages previously described in Western red colobus (Procolobus badius badius) or black-and-white colobus (Colobus guereza). Phylogenetic analyses of host mitochondrial DNA sequences revealed that red colobus populations in East and West Africa diverged from one another approximately 4.25 million years ago. These results indicate that geographic subdivisions within the red colobus taxonomic complex exert a strong influence on retroviral phylogeny and that studying retroviral diversity in closely related primate taxa should be particularly informative for understanding host-virus coevolution. PMID:19692478

Palaeogeography of Late Triassic red-beds in Singapore and the Indosinian Orogeny

NASA Astrophysics Data System (ADS)

Oliver, Grahame; Prave, Anthony

2013-10-01

A red-bed facies of the Upper Triassic Jurong Formation has been logged on Sentosa Island, Singapore. An overall coarsening and thickening-upward pattern is well developed. The lower part of the section is dominated by purple-red, massive to finely laminated illite-smectite-kaolin-rich mudstones containing thin, discontinuous lenses of fine sandstone marked by low-angle lamination and small ripples. One dinosaur-like foot print has been discovered in a loose block of red mudstone. It is concluded that this is a lacustrine sequence and it is proposed to name the lake, Lake Sentosa. The upper part of the sequence consists of flat-laminated to trough cross-bedded medium-grained sandstone and granule to cobble conglomerates alternating with purple-red mudstone. The mudstone-sandstone packages are arranged in decametre-scale coarsening-upward cycles. The channelling and decimetre-scale cross-bedding characterising the sandstone and conglomeratic beds is evidence for deposition by flashy fluvial flood processes, possibly feeding into the lake as a fresh water delta. One possible dinosaur trackway in granule size conglomerate has been located. Detrital zircon U-Pb ages vary from 2.7 Ba to 209 Ma with significant populations at ˜245 Ma and 220 Ma. These ages throw light on the timing of the Indosinian Orogeny. The molasse red-beds of the Jurong Formation were deposited in a half graben formed in the hangingwall of the Bukit Timah Fault when central Peninsular Malaysia went into extension following the climax of the Indosinian Orogeny in the Late Triassic.

Identification of Quantitative Trait Loci for Resistance to RSIVD in Red Sea Bream (Pagrus major).

PubMed

Sawayama, Eitaro; Tanizawa, Shiho; Kitamura, Shin-Ichi; Nakayama, Kei; Ohta, Kohei; Ozaki, Akiyuki; Takagi, Motohiro

2017-12-01

Red sea bream iridoviral disease (RSIVD) is a major viral disease in red sea bream farming in Japan. Previously, we identified one candidate male individual of red sea bream that was significantly associated with convalescent individuals after RSIVD. The purpose of this study is to identify the quantitative trait loci (QTL) linked to the RSIVD-resistant trait for future marker-assisted selection (MAS). Two test families were developed using the candidate male in 2014 (Fam-2014) and 2015 (Fam-2015). These test families were challenged with RSIV, and phenotypes were evaluated. Then, de novo genome sequences of red sea bream were obtained through next-generation sequencing, and microsatellite markers were searched and selected for linkage map construction. One immune-related gene, MHC class IIβ, was also used for linkage map construction. Of the microsatellite markers searched, 148 and 197 were mapped on 23 and 27 linkage groups in the female and male linkage maps, respectively, covering approximately 65% of genomes in both sexes. One QTL linked to an RSIVD-resistant trait was found in linkage group 2 of the candidate male in Fam-2014, and the phenotypic variance of the QTL was 31.1%. The QTL was closely linked to MHC class IIβ. Moreover, the QTL observed in Fam-2014 was also significantly linked to an RSIVD-resistant trait in the candidate male of Fam-2015. Our results suggest that the RSIVD-resistant trait in the candidate male was controlled by one major QTL closely linked to the MHC class IIβ gene and could be useful for MAS of red sea bream.

Genetic Basis for Red Coloration in Birds.

PubMed

Lopes, Ricardo J; Johnson, James D; Toomey, Matthew B; Ferreira, Mafalda S; Araujo, Pedro M; Melo-Ferreira, José; Andersson, Leif; Hill, Geoffrey E; Corbo, Joseph C; Carneiro, Miguel

2016-06-06

The yellow and red feather pigmentation of many bird species [1] plays pivotal roles in social signaling and mate choice [2, 3]. To produce red pigments, birds ingest yellow carotenoids and endogenously convert them into red ketocarotenoids via an oxidation reaction catalyzed by a previously unknown ketolase [4-6]. We investigated the genetic basis for red coloration in birds using whole-genome sequencing of red siskins (Spinus cucullata), common canaries (Serinus canaria), and "red factor" canaries, which are the hybrid product of crossing red siskins with common canaries [7]. We identified two genomic regions introgressed from red siskins into red factor canaries that are required for red coloration. One of these regions contains a gene encoding a cytochrome P450 enzyme, CYP2J19. Transcriptome analysis demonstrates that CYP2J19 is significantly upregulated in the skin and liver of red factor canaries, strongly implicating CYP2J19 as the ketolase that mediates red coloration in birds. Interestingly, a second introgressed region required for red feathers resides within the epidermal differentiation complex, a cluster of genes involved in development of the integument. Lastly, we present evidence that CYP2J19 is involved in ketocarotenoid formation in the retina. The discovery of the carotenoid ketolase has important implications for understanding sensory function and signaling mediated by carotenoid pigmentation. Copyright © 2016 Elsevier Ltd. All rights reserved.

X-ray versus infrared selection of distant galaxy clusters: a case study using the XMM-LSS and SpARCS cluster samples

NASA Astrophysics Data System (ADS)

Willis, J. P.; Ramos-Ceja, M. E.; Muzzin, A.; Pacaud, F.; Yee, H. K. C.; Wilson, G.

2018-07-01

We present a comparison of two samples of z> 0.8 galaxy clusters selected using different wavelength-dependent techniques and examine the physical differences between them. We consider 18 clusters from the X-ray-selected XMM Large Scale Structure (LSS) distant cluster survey and 92 clusters from the optical-mid-infrared (MIR)-selected Spitzer Adaptation of the Red Sequence Cluster survey (SpARCS) cluster survey. Both samples are selected from the same approximately 9 sq deg sky area and we examine them using common XMM-Newton, Spitizer Wide-Area Infrared Extra-galactic (SWIRE) survey, and Canada-France-Hawaii Telescope Legacy Survey data. Clusters from each sample are compared employing aperture measures of X-ray and MIR emission. We divide the SpARCS distant cluster sample into three sub-samples: (i) X-ray bright, (ii) X-ray faint, MIR bright, and (iii) X-ray faint, MIR faint clusters. We determine that X-ray- and MIR-selected clusters display very similar surface brightness distributions of galaxy MIR light. In addition, the average location and amplitude of the galaxy red sequence as measured from stacked colour histograms is very similar in the X-ray- and MIR-selected samples. The sub-sample of X-ray faint, MIR bright clusters displays a distribution of brightest cluster galaxy-barycentre position offsets which extends to higher values than all other samples. This observation indicates that such clusters may exist in a more disturbed state compared to the majority of the distant cluster population sampled by XMM-LSS and SpARCS. This conclusion is supported by stacked X-ray images for the X-ray faint, MIR bright cluster sub-sample that display weak, centrally concentrated X-ray emission, consistent with a population of growing clusters accreting from an extended envelope of material.

Genome sequencing and analyses of the postharvest fungus Penicillium expansum R21

USDA-ARS?s Scientific Manuscript database

Blue mold is the vernacular name of a common postharvest disease of stored apples, pears and quince that is caused by several common species of Penicillium. This study reports the draft genome sequence of Penicillium expansum strain R21, a strain isolated from a Red Delicious apple in 2011 in Pennsy...

Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.).

PubMed

Guo, Yinshan; Shi, Guangli; Liu, Zhendong; Zhao, Yuhui; Yang, Xiaoxu; Zhu, Junchi; Li, Kun; Guo, Xiuwu

2015-01-01

In this study, 149 F1 plants from the interspecific cross between 'Red Globe' (Vitis vinifera L.) and 'Shuangyou' (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for 'Red Globe,' 63.65 for 'Shuangyou,' and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape.

A sample of potential disk hosting first ascent red giants

NASA Astrophysics Data System (ADS)

Steele, Amy; Debes, John

2018-01-01

Observations of (sub)giants with planets and disks provide the first set of proof that disks can survive the first stages of post-main-sequence evolution, even though the disks are expected to dissipate by this time. The infrared (IR) excesses present around a number of post-main-sequence (PMS) stars could be due to a traditional debris disk with planets (e.g. kappa CrB), some remnant of enhanced mass loss (e.g. the shell-like structure of R Sculptoris), and/or background contamination. We present a sample of potential disk hosting first ascent red giants. These stars all have infrared excesses at 22 microns, and possibly host circumstellar debris. We summarize the characteristics of the sample to better inform the incidence rates of thermally emitting material around giant stars. A thorough follow-up study of these candidates would serve as the first step in probing the composition of the dust in these systems that have left the main sequence, providing clues to the degree of disk processing that occurs beyond the main-sequence.

The dust masses in the remnants of Cas A, SN1993J and SN 1980K

NASA Astrophysics Data System (ADS)

Barlow, Mike; Bevan, Antonia

2016-06-01

Using a recently developed 3D Monte Carlo dust line-scattering and absorption code, Bevan & Barlow (2016, MNRAS) have modeled the red-blue line asymmetries in the late-time Hα and [O i] spectra of SN 1987A caued by the preferential absorption by internal dust particles of redshifted photons from the far side of the ejecta. They found dust masses that grew from ≤ 10-3 M⊙ on day 714 to ≥ 0.10 M⊙ by day 3604, a trend that agrees with the day 615 - 9200 SED modeling results of Wesson et al. (2015) for SN 1987A, for which Herschel and ALMA observations indicate a dust mass of ˜0.7 M⊙ by day 9200. Similar red-blue emission line asymmetries are often observed in the late-time optical spectra of other supernova ejecta and remnants. With the aim of increasing the number of SNR dust mass determinations, we have modeled the red-blue emission line asymmetries in the late-time optical spectra of SN 1993J and SN 1980K published by Milisavljevic & Fesen (2013), as well as modeling similar red-blue line asymmetries seen in the integrated optical spectrum of Cas A published by Milisavljevic et al. (2013). Depending on grain composition, clumped dust masses of 0.1-0.4 M⊙ are required to provide fits to the Year-31 Hα and [O i] line profiles of SN 1980K, while fits to the Year-16 [O ii] and [O iii] line profiles of SN 1993J require up to 0.18 M⊙ of clumped ejecta dust. For Cas A, the fits to its [O i], [O ii] and [O iii] integrated line profiles require about 1 M⊙ of internal dust to be present.

A Single Molecule Scaffold for the Maize Genome

PubMed Central

Zhou, Shiguo; Wei, Fusheng; Nguyen, John; Bechner, Mike; Potamousis, Konstantinos; Goldstein, Steve; Pape, Louise; Mehan, Michael R.; Churas, Chris; Pasternak, Shiran; Forrest, Dan K.; Wise, Roger; Ware, Doreen; Wing, Rod A.; Waterman, Michael S.; Livny, Miron; Schwartz, David C.

2009-01-01

About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy, gene-coding sequences. The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map (iMap), but this resource alone was not sufficient for ensuring the quality of the current sequence build. For this purpose, we constructed a genome-wide, high-resolution optical map of the maize inbred line B73 genome containing >91,000 restriction sites (averaging 1 site/∼23 kb) accrued from mapping genomic DNA molecules. Our optical map comprises 66 contigs, averaging 31.88 Mb in size and spanning 91.5% (2,103.93 Mb/∼2,300 Mb) of the maize genome. A new algorithm was created that considered both optical map and unfinished BAC sequence data for placing 60/66 (2,032.42 Mb) optical map contigs onto the maize iMap. The alignment of optical maps against numerous data sources yielded comprehensive results that proved revealing and productive. For example, gaps were uncovered and characterized within the iMap, the FPC (fingerprinted contigs) map, and the chromosome-wide pseudomolecules. Such alignments also suggested amended placements of FPC contigs on the maize genetic map and proactively guided the assembly of chromosome-wide pseudomolecules, especially within complex genomic regions. Lastly, we think that the full integration of B73 optical maps with the maize iMap would greatly facilitate maize sequence finishing efforts that would make it a valuable reference for comparative studies among cereals, or other maize inbred lines and cultivars. PMID:19936062

Microbial genome sequencing using optical mapping and Illumina sequencing

USDA-ARS?s Scientific Manuscript database

Introduction Optical mapping is a technique in which strands of genomic DNA are digested with one or more restriction enzymes, and a physical map of the genome constructed from the resulting image. In outline, genomic DNA is extracted from a pure culture, linearly arrayed on a specialized glass sli...

Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach

PubMed Central

Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

2015-01-01

Abstract Objective Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Methods Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR–RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. Results PCR–RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR–RED. Conclusion NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR–RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's already known about this topic? Non-invasive prenatal diagnosis (NIPD) using PCR-based methods has been reported for the detection or exclusion of individual paternally inherited or de novo alleles in maternal plasma. What does this study add? NIPD using next generation sequencing provides an accurate, more sensitive approach which can be used to detect multiple mutations in a single assay and so is ideal when screening a gene with multiple potential pathogenic mutations. Next generation sequencing thus provides a flexible approach to non-invasive prenatal diagnosis ideal for use in a busy service laboratory. PMID:25728633

Resistance to Change and Preference for Variable versus Fixed Response Sequences

ERIC Educational Resources Information Center

Arantes, Joana; Berg, Mark E.; Le, Dien; Grace, Randolph C.

2012-01-01

In Experiment 1, 4 pigeons were trained on a multiple chain schedule in which the initial link was a variable-interval (VI) 20-s schedule signalled by a red or green center key, and terminal links required four responses made to the left (L) and/or right (R) keys. In the REPEAT component, signalled by red keylights, only LRLR terminal-link…

Molecular and histopathological detection of Hepatozoon canis in red foxes (Vulpes vulpes) from Portugal.

PubMed

Cardoso, Luís; Cortes, Helder C E; Eyal, Osnat; Reis, Antónia; Lopes, Ana Patrícia; Vila-Viçosa, Maria João; Rodrigues, Paula A; Baneth, Gad

2014-03-24

Hepatozoon canis is a protozoan tick-borne pathogen of dogs and wild canids. Hepatozoon spp. have been reported to infect foxes in different continents and recent studies have mostly used the polymerase chain reaction (PCR) for the detection and characterization of the infecting species. Surveying red foxes (Vulpes vulpes) may contribute to better understanding the epidemiology of canine vector-borne diseases, including hepatozoonosis caused by H. canis in domestic dogs. The present study investigated the prevalence of Hepatozoon spp. by means of histopathology and molecular analysis of different tissues in red foxes from different parts of Portugal. Blood and tissues including bone marrow, heart, hind leg muscle, jejunum, kidney, liver, lung, popliteal or axillary lymph nodes, spleen and/or tongue were collected from 91 red foxes from eight districts in northern, central and southern Portugal. Tissues were formalin-fixed, paraffin-embedded, cut and stained with hematoxylin and eosin. Polymerase chain reaction (PCR) amplified a ~650 bp fragment of the 18S rRNA gene of Hepatozoon spp. and the DNA products were sequenced. Hepatozoon canis was detected in 68 out of 90 foxes (75.6%) from all the sampled areas by PCR and sequencing. Histopathology revealed H. canis meronts similar in shape to those found in dogs in the bone marrow of 11 (23.4%) and in the spleen of two (4.3%) out of 47 foxes (p = 0.007). All the 11 foxes found positive by histopathology were also positive by PCR of bone marrow and/or blood. Positivity by PCR (83.0%) was significantly higher (p < 0.001) than by histopathological examination (23.4%) in paired bone marrow samples from the same 47 foxes. Sequences of the 18S rRNA gene of H. canis were 98-99% identical to those in GenBank. Hepatozoon canis was found to be highly prevalent in red fox populations from northern, central and southern Portugal. Detection of the parasite by histopathology was significantly less sensitive than by PCR. Red foxes are a presumptive reservoir of H. canis infection for domestic dogs.

Molecular and histopathological detection of Hepatozoon canis in red foxes (Vulpes vulpes) from Portugal

PubMed Central

2014-01-01

Background Hepatozoon canis is a protozoan tick-borne pathogen of dogs and wild canids. Hepatozoon spp. have been reported to infect foxes in different continents and recent studies have mostly used the polymerase chain reaction (PCR) for the detection and characterization of the infecting species. Surveying red foxes (Vulpes vulpes) may contribute to better understanding the epidemiology of canine vector-borne diseases, including hepatozoonosis caused by H. canis in domestic dogs. The present study investigated the prevalence of Hepatozoon spp. by means of histopathology and molecular analysis of different tissues in red foxes from different parts of Portugal. Methods Blood and tissues including bone marrow, heart, hind leg muscle, jejunum, kidney, liver, lung, popliteal or axillary lymph nodes, spleen and/or tongue were collected from 91 red foxes from eight districts in northern, central and southern Portugal. Tissues were formalin-fixed, paraffin-embedded, cut and stained with hematoxylin and eosin. Polymerase chain reaction (PCR) amplified a ~650 bp fragment of the 18S rRNA gene of Hepatozoon spp. and the DNA products were sequenced. Results Hepatozoon canis was detected in 68 out of 90 foxes (75.6%) from all the sampled areas by PCR and sequencing. Histopathology revealed H. canis meronts similar in shape to those found in dogs in the bone marrow of 11 (23.4%) and in the spleen of two (4.3%) out of 47 foxes (p = 0.007). All the 11 foxes found positive by histopathology were also positive by PCR of bone marrow and/or blood. Positivity by PCR (83.0%) was significantly higher (p < 0.001) than by histopathological examination (23.4%) in paired bone marrow samples from the same 47 foxes. Sequences of the 18S rRNA gene of H. canis were 98–99% identical to those in GenBank. Conclusions Hepatozoon canis was found to be highly prevalent in red fox populations from northern, central and southern Portugal. Detection of the parasite by histopathology was significantly less sensitive than by PCR. Red foxes are a presumptive reservoir of H. canis infection for domestic dogs. PMID:24655375

AKARI OBSERVATION OF THE NORTH ECLIPTIC POLE (NEP) SUPERCLUSTER AT z = 0.087: MID-INFRARED VIEW OF TRANSITION GALAXIES

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

Ko, Jongwan; Im, Myungshin; Lee, Hyung Mok

2012-02-01

We present the mid-infrared (MIR) properties of galaxies within a supercluster in the north ecliptic pole region at z {approx} 0.087 observed with the AKARI satellite. We use data from the AKARI NEP-Wide (5.4 deg{sup 2}) IR survey and the CLusters of galaxies EVoLution studies (CLEVL) mission program. We show that near-IR (3 {mu}m)-mid-IR (11 {mu}m) color can be used as an indicator of the specific star formation rate and the presence of intermediate-age stellar populations. From the MIR observations, we find that red-sequence galaxies consist not only of passively evolving red early-type galaxies, but also of (1) 'weak-SFGs' (disk-dominatedmore » star-forming galaxies that have star formation rates lower by {approx}4 Multiplication-Sign than blue-cloud galaxies) and (2) 'intermediate-MXGs' (bulge-dominated galaxies showing stronger MIR dust emission than normal red early-type galaxies). These two populations can be a set of transition galaxies from blue, star-forming, late-type galaxies evolving into red, quiescent, early-type ones. We find that the weak-SFGs are predominant at intermediate masses (10{sup 10} M{sub Sun} < M{sub *} < 10{sup 10.5} M{sub Sun }) and are typically found in local densities similar to the outskirts of galaxy clusters. As much as 40% of the supercluster member galaxies in this mass range can be classified as weak-SFGs, but their proportion decreases to <10% at larger masses (M{sub *} > 10{sup 10.5} M{sub Sun }) at any galaxy density. The fraction of the intermediate-MXG among red-sequence galaxies at 10{sup 10} M{sub Sun} < M{sub *} < 10{sup 11} M{sub Sun} also decreases as the density and mass increase. In particular, {approx}42% of the red-sequence galaxies with early-type morphologies are classified as intermediate-MXGs at intermediate densities. These results suggest that the star formation activity is strongly dependent on the stellar mass, but that the morphological transformation is mainly controlled by the environment.« less

Non-invasive red light optogenetic pacing and optical coherence microscopy (OCM) imaging for drosophila melanogaster (Conference Presentation)

NASA Astrophysics Data System (ADS)

Men, Jing; Li, Airong; Jerwick, Jason; Tanzi, Rudolph E.; Zhou, Chao

2017-02-01

Cardiac pacing could be a powerful tool for investigating mammalian cardiac electrical conduction systems as well as for treatment of certain cardiac pathologies. However, traditional electrical pacing using pacemaker requires an invasive surgical procedure. Electrical currents from the implanted electrodes can also cause damage to heart tissue, further restricting its utility. Optogenetic pacing has been developed as a promising, non-invasive alternative to electrical stimulation for controlling animal heart rhythms. It induces heart contractions by shining pulsed light on transgene-generated microbial opsins, which in turn activate the light gated ion channels in animal hearts. However, commonly used opsins in optogenetic pacing, such as channelrhodopsin-2 (ChR2), require short light wavelength stimulation (475 nm), which is strongly absorbed and scattered by tissue. Here, we performed optogenetic pacing by expression of recently engineered red-shifted microbial opsins, ReaChR and CsChrimson, in a well-established animal model, Drosophila melanogaster, using the 617 nm stimulation light pulses. The OCM technique enables non-invasive optical imaging of animal hearts with high speed and ultrahigh axial and transverse resolutions. We integrated a customized OCM system with the optical stimulation system to monitor the optogenetic pacing noninvasively. The use of red-sifted opsins enabled deeper penetration of simulating light at lower power, which is promising for applications of optogenetic pacing in mammalian cardiac pathology studies or clinical treatments in the future.

Jahn-Teller distortion of Mn3+-occupied octahedra in red beryl from Utah indicated by optical spectroscopy

NASA Astrophysics Data System (ADS)

Fridrichová, Jana; Bačík, Peter; Ertl, Andreas; Wildner, Manfred; Dekan, Július; Miglierini, Marcel

2018-01-01

Red beryl from Utah is chemically homogeneous and contains only Fe < 0.163, Mn < 0.018, and Mg < 0.016 apfu. Channel sites contain only up to Cs 0.011, K 0.009, Rb 0.004, and Na 0.004 apfu. This suggests only very slight tetrahedral (Cs,K,Rb)Li□-1Be-1 substitution, octahedral Na(Fe2+,Mg)□-1Al-1 substitution can be excluded. Fe and Mn are trivalent as documented by Mössbauer spectroscopy and optical absorption spectroscopy. Red beryl optimized formula is ∼[(Cs,Rb,K)0.02□0.98]Σ1.00□1.00(Al1.79Fe3+0.16Mn3+0.02Ti4+0.02Mg0.01)Σ2.00Be3(Si6O18). Location of Mn3+ was estimated to the octahedral Al3+ site, other choices are improbable due to the bond-length requirements. No Mn3+-induced Jahn-Teller structural distortion was detected due to site symmetry restrictions and small Mn3+ content. However, optical spectroscopy shows broad band at ∼7190 cm-1 assigned to the excited level of the spin-allowed pseudo-tetragonal split E ground state of elongated six-fold Mn3+ coordination. Crystal field calculations indicate that the local Mn3+ environment complies well with crystal chemical expectations for Jahn-Teller distorted Mn3+O6 octahedra.

The visible, near-infrared and short wave infrared channels of the EarthCARE multi-spectral imager

NASA Astrophysics Data System (ADS)

Doornink, J.; de Goeij, B.; Marinescu, O.; Meijer, E.; Vink, R.; van Werkhoven, W.; van't Hof, A.

2017-11-01

The EarthCARE satellite mission objective is the observation of clouds and aerosols from low Earth orbit. The payload will include active remote sensing instruments being the W-band Cloud Profiling Radar (CPR) and the ATLID LIDAR. These are supported by the passive instruments Broadband Radiometer (BBR) and the Multispectral Imager (MSI) providing the radiometric and spatial context of the ground scene being probed. The MSI will form Earth images over a swath width of 150 km; it will image the Earth atmosphere in 7 spectral bands. The MSI instrument consists of two parts: the Visible, Near infrared and Short wave infrared (VNS) unit, and the Thermal InfraRed (TIR) unit. Subject of this paper is the VNS unit. In the VNS optical unit, the ground scene is imaged in four spectral bands onto four linear detectors via separate optical channels. Driving requirements for the VNS instrument performance are the spectral sensitivity including out-of-band rejection, the MTF, co-registration and the inter-channel radiometric accuracy. The radiometric accuracy performance of the VNS is supported by in-orbit calibration, in which direct solar radiation is fed into the instrument via a set of quasi volume diffusers. The compact optical concept with challenging stability requirements together with the strict thermal constraints have led to a sophisticated opto-mechanical design. This paper, being the second of a sequence of two on the Multispectral Imager describes the VNS instrument concept chosen to fulfil the performance requirements within the resource and accommodation constraints.

A novel optical probe for pH sensing in gastro-esophageal apparatus

NASA Astrophysics Data System (ADS)

Baldini, F.; Ghini, G.; Giannetti, A.; Senesi, F.; Trono, C.

2011-03-01

Monitoring gastric pH for long periods, usually 24 h, may be essential in analyzing the physiological pattern of acidity, in obtaining information on changes in activity during peptic ulcer disease, and in assessing the effect of antisecretory drugs. Gastro-esophageal reflux, which causes a pH decrease in the esophagus content from pH 7 even down to pH 2, can determine esophagitis with possible strictures and Barrett's esophagus. One of the difficulties of the optical measurement of pH in the gastro-esophageal apparatus lies in the required extended working range from 1 to 8 pH units. The present paper deals with a novel optical pH sensor, using methyl red as optical pH indicator. Contrary to all acidbase indicators characterized by working ranges limited to 2-3 pH units, methyl red, after its covalent immobilization on controlled pore glass (CPG), is characterized by a wide working range which fits with the clinical requirements. The novel probe design here described is suitable for gastro-esophageal applications and allows the optimization of the performances of the CPG with the immobilised indicator. This leads to a very simple configuration characterized by a very fast response time.

DISCOVERY OF A POSSIBLE COOL WHITE DWARF COMPANION FROM THE AllWISE MOTION SURVEY

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

Fajardo-Acosta, Sergio B.; Kirkpatrick, J. Davy; Gelino, Christopher R.

We present optical and near-infrared spectroscopy of WISEA J061543.91-124726.8, which we rediscovered as a high motion object in the AllWISE survey. The spectra of this object are unusual; while the red optical ( λ > 7000 Å) and near-infrared spectra exhibit characteristic TiO, VO, and H{sub 2}O bands of a late-M dwarf, the blue portion of its optical spectrum shows a significant excess of emission relative to late-M-type templates. The excess emission is relatively featureless, with the exception of a prominent and very broad Na i D doublet. We find that no single, ordinary star can reproduce these spectral characteristics.more » The most likely explanation is an unresolved binary system of an M7 dwarf and a cool white dwarf. The flux of a cool white dwarf drops in the optical red and near-infrared, due to collision-induced absorption, thus allowing the flux of a late-M dwarf to show through. This scenario, however, does not explain the Na D feature, which is unlike that of any known white dwarf, but which could perhaps be explained via unusual abundance or pressure conditions.« less

Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure.

PubMed

Donaldson, Michael E; Rico, Yessica; Hueffer, Karsten; Rando, Halie M; Kukekova, Anna V; Kyle, Christopher J

2018-01-01

Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization-based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to "capture" specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300-kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on-target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer-read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune-related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.

Evolutionary paths among different red galaxy types at 0.3 < z < 1.5 and the build-up of massive E-S0's

NASA Astrophysics Data System (ADS)

Gallego, Jesús; Prieto, Mercedes; Eliche-Moral, M. Carmen; Balcells, Marc; Cristóbal-Hornillos, David; Erwin, Peter; Abreu, David; Domínguez-Palmero, Lilian; Hempel, Angela; López-Sanjuan, Carlos; Guzmán, Rafael; Pérez-González, Pablo G.; Barro, Guillermo; Zamorano, Jaime

2013-07-01

Some recent observations seem to disagree with hierarchical theories of galaxy formation on the role of major mergers in a late build-up of massive early-type galaxies. We re-address this question by analysing the morphology, structural distortion level, and star formation enhancement of a sample of massive galaxies (M* > 5 × 1010M⊙) lying on the Red Sequence and its surroundings at 0.3 < z < 1.5. We have used an initial sample of ~1800 sources with Ks < 20.5 mag over an area ~155 arcmin2 on the Groth Strip, combining data from the Rainbow Extragalactic Database and the GOYA Survey. Red galaxy classes that can be directly associated to intermediate stages of major mergers and to their final products have been defined. For the first time we report observationally the existence of a dominant evolutionary path among massive red galaxies at 0.6 < z < 1.5, consisting in the conversion of irregular disks into irregular spheroids, and of these ones into regular spheroids. This result points to: 1) the massive red regular galaxies at low redshifts derive from the irregular ones populating the Red Sequence and its neighbourhood at earlier epochs up to z ~ 1.5; 2) the progenitors of the bulk of present-day massive red regular galaxies have been blue disks that have migrated to the Red Sequence majoritarily through major mergers at 0.6 < z < 1.2 (these mergers thus starting at z ~ 1.5); 3) the formation of E-S0's that end up with M* > 1011M⊙ at z = 0 through gas-rich major mergers has frozen since z ~ 0.6. Our results support that major mergers have played the dominant role in the definitive build-up of present-day E-S0's with M* > 1011M⊙ at 0.6 < z < 1.2, in good agreement with the hierarchical scenario proposed in the Eliche-Moral et al. (2010a) model (see also Eliche-Moral et al. 2010b). This study is published in Prieto et al. (2012). Supported by the Spanish Ministry of Science and Innovation (MICINN) under projects AYA2009-10368, AYA2006-12955, AYA2010-21887-C04-04, and AYA2009-11137, by the Madrid Regional Government through the AstroMadrid Project (CAM S2009/ESP-1496), and by the Spanish MICINN under the Consolider-Ingenio 2010 Program grant CSD2006-00070: ``First Science with the GTC'' (http://www.iac.es/consolider-ingenio-gtc/). S. D. H. & G.

Design of pseudorandom binary sequence generator using lithium-niobate-based Mach-Zehnder interferometers

NASA Astrophysics Data System (ADS)

Choudhary, Kuldeep; Kumar, Santosh

2017-05-01

The application of electro-optic effect in lithium-niobate-based Mach-Zehnder interferometer to design a 3-bit optical pseudorandom binary sequence (PRBS) generator has been proposed, which is characterized by its simplicity of generation and stability. The proposed device is optoelectronic in nature. The PBRS generator is immensely applicable for pattern generation, encryption, and coding applications in optical networks. The study is carried out by simulating the proposed device with beam propagation method.

SNP discovery and High Resolution Melting Analysis from massive transcriptome sequencing in the California red abalone Haliotis rufescens.

PubMed

Valenzuela-Muñoz, Valentina; Araya-Garay, José Miguel; Gallardo-Escárate, Cristian

2013-06-01

The California red abalone, Haliotis rufescens that belongs to the Haliotidae family, is the largest species of abalone in the world that has sustained the major fishery and aquaculture production in the USA and Mexico. This native mollusk has not been evaluated or assigned a conservation category even though in the last few decades it was heavily exploited until it disappeared in some areas along the California coast. In Chile, the red abalone was introduced in the 1970s from California wild abalone stocks for the purposes of aquaculture. Considering the number of years that the red abalone has been cultivated in Chile crucial genetic information is scarce and critical issues remain unresolved. This study reports and validates novel single nucleotide polymorphisms (SNP) markers for the red abalone H. rufescens using cDNA pyrosequencing. A total of 622 high quality SNPs were identified in 146 sequences with an estimated frequency of 1 SNP each 1000bp. Forty-five SNPs markers with functional information for gene ontology were selected. Of these, 8 were polymorphic among the individuals screened: Heat shock protein 70 (HSP70), vitellogenin (VTG), lysin, alginate lyase enzyme (AL), Glucose-regulated protein 94 (GRP94), fructose-bisphosphate aldolase (FBA), sulfatase 1A precursor (S1AP) and ornithine decarboxylase antizyme (ODC). Two additional sequences were also identified with polymorphisms but no similarities with known proteins were achieved. To validate the putative SNP markers, High Resolution Melting Analysis (HRMA) was conducted in a wild and hatchery-bred population. Additionally, SNP cross-amplifications were tested in two further native abalone species, Haliotis fulgens and Haliotis corrugata. This study provides novel candidate genes that could be used to evaluate loss of genetic diversity due to hatchery selection or inbreeding effects. Copyright © 2013 Elsevier B.V. All rights reserved.

UV light induced red emission in Eu3+-doped zincborophosphate glasses

NASA Astrophysics Data System (ADS)

Hima Bindu, S.; Siva Raju, D.; Vinay Krishna, V.; Rajavardhana Rao, T.; Veerabrahmam, K.; Linga Raju, Ch.

2016-12-01

This paper reports the preparation of transparent zincborophosphate (ZBP) glasses doped with Eu3+ ions by the conventional melt quenching technique. The prepared glasses were characterized using powder XRD, FTIR, optical absorption, photoluminescence and decay curves. Judd-Ofelt (JO) intensity parameters calculated under various constraints using absorption and emission spectra. These JO intensity parameters have been used to predict the radiative properties such as radiative life time, branching ratios and stimulated emission cross section of the 5D0→7FJ (J = 0-4) transitions. Decay curves for the 5D0 level of Eu3+ ions shows single exponential for all concentrations. Luminescence properties of 5D0→7F2 transitions of Eu3+ions have revealed that the present ZBP:Eu3+ glasses have significant in optical applications at around 613 nm. An intense red luminescence has been observed due to 5D0→7F2 transition of Eu3+ ion in these glasses. From the CIE color coordinate diagram, it is observed that the present glass system is prominent material for red emission.

Design and optimization of a volume-phase holographic grating for simultaneous use with red, green, and blue light using unpolarized light.

PubMed

Mahamat, Adoum H; Narducci, Frank A; Schwiegerling, James

2016-03-01

Volume-phase holographic (VPH) gratings have been designed for use in many areas of science and technology, such as optical communication, optical imaging, and astronomy. In this paper, the design of a volume-phase holographic grating, simultaneously optimized to operate in the red, green, and blue wavelengths, is presented along with a study of its fabrication tolerances. The grating is optimized to produce 98% efficiency at λ=532  nm and at least 75% efficiency in the region between 400 and 700 nm, when the incident light is unpolarized. The optimization is done for recording in dichromated gelatin with a thickness of 12 μm, an average refractive index of 1.5, and a refractive index modulation of 0.022.

Study of porous silicon optical waveguides impregnated with organic dyes

NASA Astrophysics Data System (ADS)

Pirasteh, P.; Charrier, J.; Dumeige, Y.; Chaillou, A.; Guendouz, M.; Haji, L.

2007-01-01

Planar waveguides were made using oxidised porous silicon layers. Then, they were impregnated with Congo Red or Disperse Red 1 dyes. Optical losses were investigated before and after impregnation. In our case, the losses of impregnated waveguides were always higher than those of non-impregnated ones. In order to achieve a better understanding of the origin of these losses, we not only studied the absorbance of solutions which would impregnate the porous layers but also the reflectance spectra of the obtained composite materials. According to the measurements, the increase in losses in the visible spectrum depends on the intrinsic absorption of the dye while in NIR, the increase would be due to an accumulation of dried dye on the surface of the waveguide which would give rise to the surface scattering losses.

Stretching of red blood cells using an electro-optics trap.

PubMed

Haque, Md Mozzammel; Moisescu, Mihaela G; Valkai, Sándor; Dér, András; Savopol, Tudor

2015-01-01

The stretching stiffness of Red Blood Cells (RBCs) was investigated using a combination of an AC dielectrophoretic apparatus and a single-beam optical tweezer. The experiments were performed at 10 MHz, a frequency high enough to avoid conductivity losses, but below the second turnover point between positive and negative dielectrophoresis. By measuring the geometrical parameters of single healthy human RBCs as a function of the applied voltage, the elastic modulus of RBCs was determined (µ = 1.80 ± 0.5 µN/m) and compared with similar values of the literature got by other techniques. The method is expected to be an easy-to-use, alternative tool to determine the mechano-elastic properties of living cells, and, on this basis, to distinguish healthy and diseased cells.

Capillary red blood cell velocimetry by phase-resolved optical coherence tomography.

PubMed

Tang, Jianbo; Erdener, Sefik Evren; Fu, Buyin; Boas, David A

2017-10-01

We present a phase-resolved optical coherence tomography (OCT) method to extend Doppler OCT for the accurate measurement of the red blood cell (RBC) velocity in cerebral capillaries. OCT data were acquired with an M-mode scanning strategy (repeated A-scans) to account for the single-file passage of RBCs in a capillary, which were then high-pass filtered to remove the stationary component of the signal to ensure an accurate measurement of phase shift of flowing RBCs. The angular frequency of the signal from flowing RBCs was then quantified from the dynamic component of the signal and used to calculate the axial speed of flowing RBCs in capillaries. We validated our measurement by RBC passage velocimetry using the signal magnitude of the same OCT time series data.

Multi-particle three-dimensional coordinate estimation in real-time optical manipulation

NASA Astrophysics Data System (ADS)

Dam, J. S.; Perch-Nielsen, I.; Palima, D.; Gluckstad, J.

2009-11-01

We have previously shown how stereoscopic images can be obtained in our three-dimensional optical micromanipulation system [J. S. Dam et al, Opt. Express 16, 7244 (2008)]. Here, we present an extension and application of this principle to automatically gather the three-dimensional coordinates for all trapped particles with high tracking range and high reliability without requiring user calibration. Through deconvolving of the red, green, and blue colour planes to correct for bleeding between colour planes, we show that we can extend the system to also utilize green illumination, in addition to the blue and red. Applying the green colour as on-axis illumination yields redundant information for enhanced error correction, which is used to verify the gathered data, resulting in reliable coordinates as well as producing visually attractive images.

Quantifying the Energy Efficiency of Object Recognition and Optical Flow

DTIC Science & Technology

2014-03-28

other linear solvers, such as conjugate- gradient (CG), preconditioned conjugate-gradient (PCG), and red-black Gauss Seidel (RB). We have also... Seidel , and conjugate gradient solvers. We are interested in the energy it takes to get a given solution quality. In Figure 6, we plot the quality of...in terms of Joules. Conversely, our implementation of red-black Gauss Seidel proves to be very inefficient when we consider Joules instead of just

Mass-losing peculiar red giants - The comparison between theory and observations

NASA Technical Reports Server (NTRS)

Jura, M.

1989-01-01

The mass loss from evolved red giants is considered. It seems that red giants on the Asymptotic Giant Branch (AGB) are losing between 0.0003 and 0.0006 solar mass/sq kpc yr in the solar neighborhood. If all the main sequence stars between 1 and 5 solar masses ultimately evolve into white dwarfs with masses of 0.7 solar mass, the predicted mass loss rate in the solar neighborhood from these stars is 0.0008 solar mass/sq kpc yr. Although there are still uncertainties, it appears that there is no strong disagreement between theory and observation.

Understanding the degradation of Congo red and bacterial diversity in an air-cathode microbial fuel cell being evaluated for simultaneous azo dye removal from wastewater and bioelectricity generation.

PubMed

Sun, Jian; Li, Youming; Hu, Yongyou; Hou, Bin; Zhang, Yaping; Li, Sizhe

2013-04-01

We investigated the mechanism of Congo red degradation and bacterial diversity in a single-chambered microbial fuel cell (MFC) incorporating a microfiltration membrane and air-cathode. The MFC was operated continuously for more than 4 months using a mixture of Congo red and glucose as fuel. We demonstrated that the Congo red azo bonds were reduced at the anode to form aromatic amines. This is consistent with the known mechanism of anaerobic biodegradation of azo dyes. The MFC developed a less dense biofilm at the anode in the presence of Congo red compared to its absence indicating that Congo red degradation negatively affected biofilm formation. Denaturing gradient gel electrophoresis and direct 16S ribosomal DNA gene nucleotide sequencing revealed that the microbial communities differed depending on whether Congo red was present in the MFC. Geobacter-like species known to generate electricity were detected in the presence or absence of Congo red. In contrast, Azospirillum, Methylobacterium, Rhodobacter, Desulfovibrio, Trichococcus, and Bacteroides species were only detected in its presence. These species were most likely responsible for degrading Congo red.

A novel all-optical label processing for OPS networks based on multiple OOC sequences from multiple-groups OOC

NASA Astrophysics Data System (ADS)

Qiu, Kun; Zhang, Chongfu; Ling, Yun; Wang, Yibo

2007-11-01

This paper proposes an all-optical label processing scheme using multiple optical orthogonal codes sequences (MOOCS) for optical packet switching (OPS) (MOOCS-OPS) networks, for the first time to the best of our knowledge. In this scheme, the multiple optical orthogonal codes (MOOC) from multiple-groups optical orthogonal codes (MGOOC) are permuted and combined to obtain the MOOCS for the optical labels, which are used to effectively enlarge the capacity of available optical codes for optical labels. The optical label processing (OLP) schemes are reviewed and analyzed, the principles of MOOCS-based optical labels for OPS networks are given, and analyzed, then the MOOCS-OPS topology and the key realization units of the MOOCS-based optical label packets are studied in detail, respectively. The performances of this novel all-optical label processing technology are analyzed, the corresponding simulation is performed. These analysis and results show that the proposed scheme can overcome the lack of available optical orthogonal codes (OOC)-based optical labels due to the limited number of single OOC for optical label with the short code length, and indicate that the MOOCS-OPS scheme is feasible.

Complete mitochondrial genomes of the yellow-bellied slider turtle Trachemys scripta scripta and anoxia tolerant red-eared slider Trachemys scripta elegans.

PubMed

Yu, Danna; Fang, Xindong; Storey, Kenneth B; Zhang, Yongpu; Zhang, Jiayong

2016-05-01

The complete mitochondrial genomes of the yellow-bellied slider (Trachemys scripta scripta) and anoxia tolerant red-eared slider (Trachemys scripta elegans) turtles were sequenced to analyze gene arrangement. The complete mt genomes of T. s. scripta and elegans were circular molecules of 16,791 bp and 16,810 bp in length, respectively, and included an A + 1 frameshift insertion in ND3 and ND4L genes. The AT content of the overall base composition of scripta and elegans was 61.2%. Nucleotide sequence divergence of the mt-genome (p distance) between scripta and elegans was 0.4%. A detailed comparison between the mitochondrial genomes of the two subspecies is shown.

Explosion of a supernova with a red giant companion

NASA Technical Reports Server (NTRS)

Livne, E.; Tuchman, Y.; Wheeler, J. C.

1992-01-01

Two-dimensional numerical simulations of the collision between spherical ejecta from a supernova and a red giant companion are presented. In contrast to previous numerical studies, in which the companion was a main-sequence star or a compact object, the collision consequences are found to have a dramatic impact upon the red giant. In most cases the red giant companion loses most of its envelope in a time scale of 10 exp 7 s with typical velocities about an order of magnitude less than those of the expanding velocity of the supernova shell. We confirm the conclusion of Chugai (1986) that the stripped hydrogen tends to come off as a low-velocity component interior to the supernova ejecta. Possible observational consequences of the results are discussed.

Mineral magnetic characteristics of the late Quaternary coastal red sands of Bheemuni, East Coast (India)

NASA Astrophysics Data System (ADS)

Srivastava, Priyeshu; Sangode, S. J.; Parmar, Nikita; Meshram, D. C.; Jadhav, Priyanka; Singhvi, A. K.

2016-11-01

The voluminous red sand deposits of Bheemuni in the east coast of India provide record of coastal land-sea interaction during the late Quaternary climatic and eustatic oscillations. Limited information on the origin and depositional environments of these red sands and their chronology is available. We studied two inland to coast cross profiles from Bheemuni red sand deposits using mineral magnetism, color characteristics and Citrate-bicarbonate-dithionite (CBD) extractable pedogenic iron oxides over 23 horizons along with optically stimulated luminescence (OSL) chronology at 6 horizons. The oldest exposed bed had an optical age of 48.9 ± 1.7 ka. Differential ages between the two parallel sections (SOS = 48.9 ± 1.7 to 12.1 ± 0.3 ka and IMD = 29.3 ± 3.5 ka) suggest laterally shifting fluvial sedimentation. Both the profiles show significant amount of antiferromagnetic oxide (hematite) along with ferrimagnetic (magnetite/maghemite) mineral composition. The granulometric (/domain-) sensitive parameters (χFD, χARM, SIRM/χLF and χARM/χLF) indicate variable concentration of superparamagnetic (SP) and single domain (SD) particles between the two profiles. The higher frequency dependent and pedogenic magnetic susceptibilities (χFD and χpedo) in the younger (IMD) profile suggest enhanced pedogenesis under a warm-wet climate post 29.3 ka and also during Holocene. A combination of hard isothermal remanent magnetization (HIRM) and redness rating (RR) index indicates distinct but variable concentration of a) crystalline and b) poorly crystalline (pigmentary) hematites in both the profiles. We consider that the former (#a) is derived from hinterland red soils and possibly due to post-depositional diagenesis, and the latter (#b) precipitated from the dissolved iron under fluvial regime imparting the unique red coloration to Bheemuni sands. Partial to complete alteration of ferromagnesian minerals due to pedogenesis in hinterlands under warm-wet climate was therefore the principal source of reddening of the Bheemuni sands.

Polarisation of the auroral red line in the Earth's upper atmosphere: a review (Invited)

NASA Astrophysics Data System (ADS)

Lamy, H.; Barthelemy, M.; Lilensten, J.; Bommier, V.; Simon Wedlund, C.

2013-12-01

Polarisation of light is a key observable to provide information about asymmetry or anisotropy within a radiative source. Polarimetry of auroral emission lines in the Earth's upper atmosphere has been overlooked for decades. However, the bright red auroral line (6300Å) produced by collisional impact with electrons precipitating along magnetic field lines is a good candidate to search for polarisation. This problem was investigated recently with observations obtained by Lilensten et al (2008), Barthélemy et al (2011) and Lilensten et al (2013) with a photopolarimeter. Analysis of the data indicates that the red auroral emission line is polarised at a level of a few percent. The results are compared to theoretical predictions of Bommier et al (2011) that were obtained for a collimated beam. The comparison suggests the existence of depolarization processes whose origin will be discussed. A new dedicated spectropolarimeter currently under development will also be presented. This instrument will cover the optical spectrum from approximately 400 to 700 nm providing simultaneously the polarisation of the red line and of other interesting auroral emission lines such as N2+ 1NG (4278Å), other N2 bands, etc... The importance of these polarisation measurements in the context of upper atmosphere modelling and geomagnetic activity will be discussed. Lilensten, J. et al, Polarization in aurorae: A new dimension for space environments studies, Geophys. Res. Lett., 26, 269, 2008 Barthélemy M. et al, Polarisation in the auroral red line during coordinated EISCAT Svalbard Radar/optical experiments, Annales Geophysicae, Volume 29, Issue 6, 2011, 1101-1112, 2011. Bommier V. et al, The Theoretical Impact Polarization of the O I 6300 Å Red Line of Earth Auroræ, Annales Geophysicae, Volume 29, Issue 1, 2011, 71-79, 2011 Lilensten, J. et al, The thermospheric auroral red line polarization: confirmation of detection and first quantitative analysis, Journal of Space Weather and Space Climate, Volume 3, 12, 2013.

Reprint of "Sequence and phylogenetic analyses of novel totivirus-like double-stranded RNAs from field-collected powdery mildew fungi".

PubMed

Kondo, Hideki; Hisano, Sakae; Chiba, Sotaro; Maruyama, Kazuyuki; Andika, Ida Bagus; Toyoda, Kazuhiro; Fujimori, Fumihiro; Suzuki, Nobuhiro

2016-07-02

The identification of mycoviruses contributes greatly to understanding of the diversity and evolutionary aspects of viruses. Powdery mildew fungi are important and widely studied obligate phytopathogenic agents, but there has been no report on mycoviruses infecting these fungi. In this study, we used a deep sequencing approach to analyze the double-stranded RNA (dsRNA) segments isolated from field-collected samples of powdery mildew fungus-infected red clover plants in Japan. Database searches identified the presence of at least ten totivirus (genus Totivirus)-like sequences, termed red clover powdery mildew-associated totiviruses (RPaTVs). The majority of these sequences shared moderate amino acid sequence identity with each other (<44%) and with other known totiviruses (<59%). Nine of these identified sequences (RPaTV1a, 1b and 2-8) resembled the genome of the prototype totivirus, Saccharomyces cerevisiae virus-L-A (ScV-L-A) in that they contained two overlapping open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA dependent RNA polymerase (RdRp), while one sequence (RPaTV9) showed similarity to another totivirus, Ustilago maydis virus H1 (UmV-H1) that encodes a single polyprotein (CP-RdRp fusion). Similar to yeast totiviruses, each ScV-L-A-like RPaTV contains a -1 ribosomal frameshift site downstream of a predicted pseudoknot structure in the overlapping region of these ORFs, suggesting that the RdRp is translated as a CP-RdRp fusion. Moreover, several ScV-L-A-like sequences were also found by searches of the transcriptome shotgun assembly (TSA) libraries from rust fungi, plants and insects. Phylogenetic analyses show that nine ScV-L-A-like RPaTVs along with ScV-L-A-like sequences derived from TSA libraries are clustered with most established members of the genus Totivirus, while one RPaTV forms a new distinct clade with UmV-H1, possibly establishing an additional genus in the family. Taken together, our results indicate the presence of diverse, novel totiviruses in the powdery mildew fungus populations infecting red clover plants in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

Ultra-fast all-optical plasmonic switching in near infra-red spectrum using a Kerr nonlinear ring resonator

NASA Astrophysics Data System (ADS)

Nurmohammadi, Tofiq; Abbasian, Karim; Yadipour, Reza

2018-03-01

In this paper, an all-optical plasmonic switch based on metal-insulator-metal (MIM) nanoplasmonic waveguide with a Kerr nonlinear ring resonator is introduced and studied. Two-dimensional simulations utilizing the finite-difference time-domain algorithm are used to demonstrate an apparent optical bistability and significant switching mechanisms (in enabled-low condition: T(ON/OFF) =21.9 and in enabled-high condition: T(ON/OFF) =24.9) of the signal light arisen by altering the pump-light intensity. The proposed all-optical switching demonstrates femtosecond-scale feedback time (90 fs) and then ultra-fast switching can be achieved. The offered all-optical switch may recognize potential significant applications in integrated optical circuits.

Intruder colour and light environment jointly determine how nesting male stickleback respond to simulated territorial intrusions.

PubMed

Bolnick, Daniel I; Hendrix, Kimberly; Jordan, Lyndon Alexander; Veen, Thor; Brock, Chad D

2016-08-01

Variation in male nuptial colour signals might be maintained by negative frequency-dependent selection. This can occur if males are more aggressive towards rivals with locally common colour phenotypes. To test this hypothesis, we introduced red or melanic three-dimensional printed-model males into the territories of nesting male stickleback from two optically distinct lakes with different coloured residents. Red-throated models were attacked more in the population with red males, while melanic models were attacked more in the melanic male lake. Aggression against red versus melanic models also varied across a depth gradient within each lake, implying that the local light environment also modulated the strength of negative frequency dependence acting on male nuptial colour. © 2016 The Author(s).

VLT/PIONIER Imaging of Red Supergiant Stars

NASA Astrophysics Data System (ADS)

Montargès, Miguel

2018-04-01

PIONIER (Precision Integrated-Optics Near-infrared Imaging ExpeRiment) was the first 4-telescope instrument installed at the Very Large Telescope Interferometer (VLTI) in 2010. Benefiting from the multiple interferometric configurations available at the Cerro Paranal observatory, it can efficiently image stellar surfaces. With their large linear sizes, nearby red supergiant stars are among the most interesting targets for such instrument. Near infrared interferometry allows to study their surface in order to get a better understanding of their mass loss, mostly by constraining the characteristics of their photospheric features. I will review recent results obtain with VLTI/PIONIER on red supergiant stars, and emphasize the different techniques used to analyze these observations.

Identification of genotyping-by-sequencing sequence tags associated with milling performance and end-use quality traits in hard red spring wheat (Triticum aestivum L.)

USDA-ARS?s Scientific Manuscript database

Wheat quality is defined by culinary end-uses and processing characteristics. Wheat breeders are interested to identify quantitative trait loci for grain, milling, and end-use quality traits because it is imperative to understand the genetic complexity underlying quantitatively inherited traits to ...

In Silico Comparative Transcriptome Analysis of Two Color Morphs of the Common Coral Trout (Plectropomus Leopardus)

PubMed Central

Wang, Le; Yu, Cuiping; Guo, Liang; Lin, Haoran; Meng, Zining

2015-01-01

The common coral trout is one species of major importance in commercial fisheries and aquaculture. Recently, two different color morphs of Plectropomus leopardus were discovered and the biological importance of the color difference is unknown. Since coral trout species are poorly characterized at the molecular level, we undertook the transcriptomic characterization of the two color morphs, one black and one red coral trout, using Illumina next generation sequencing technologies. The study produced 55162966 and 54588952 paired-end reads, for black and red trout, respectively. De novo transcriptome assembly generated 95367 and 99424 unique sequences in black and red trout, respectively, with 88813 sequences shared between them. Approximately 50% of both trancriptomes were functionally annotated by BLAST searches against protein databases. The two trancriptomes were enriched into 25 functional categories and showed similar profiles of Gene Ontology category compositions. 34110 unigenes were grouped into 259 KEGG pathways. Moreover, we identified 14649 simple sequence repeats (SSRs) and designed primers for potential application. We also discovered 130524 putative single nucleotide polymorphisms (SNPs) in the two transcriptomes, supplying potential genomic resources for the coral trout species. In addition, we identified 936 fast-evolving genes and 165 candidate genes under positive selection between the two color morphs. Finally, 38 candidate genes underlying the mechanism of color and pigmentation were also isolated. This study presents the first transcriptome resources for the common coral trout and provides basic information for the development of genomic tools for the identification, conservation, and understanding of the speciation and local adaptation of coral reef fish species. PMID:26713756

Genome-wide association studies of growth traits in three dairy cattle breeds using whole-genome sequence data.

PubMed

Mao, X; Sahana, G; De Koning, D-J; Guldbrandtsen, B

2016-04-01

Male calves and culled cows of dairy cattle are used for beef production. However, unlike beef breeds, the genetics of growth performance traits in dairy breeds have not been extensively studied. Here, we performed a genome-wide association study (GWAS) on Holsteins ( = 5,519), Jerseys ( = 1,231), and Red Dairy Cattle ( = 4,410) to identify QTL for growth traits. First, a GWAS was performed within breeds using whole-genome sequence variants. Later, a meta-analysis was performed to combine information across the 3 breeds. We have identified several QTL that have large effects on growth traits in Holsteins and Red Dairy Cattle but with little overlap across breeds. Only 1 QTL located on chromosome 10 was shared between Holsteins and Red Dairy Cattle. The most significant variant (BTA10:59,164,533, rs43636323; -value = 2.8 × 10) in this QTL explained 2.4% of the total additive genetic variance in Red Dairy Cattle. The gene is a strong candidate for the underlying gene of this QTL. In Red Dairy Cattle, a QTL near 25 Mb on chromosome 14 was very significantly associated with growth traits, consistent with the previously reported gene , which affects growth in beef cattle and humans. No QTL for growth performance was statistically significant in Jerseys, possibly due to the low power of detection with the small sample size. The meta-analysis of the 3 breeds increased the power to detect QTL.

Computational design of RNA parts, devices, and transcripts with kinetic folding algorithms implemented on multiprocessor clusters.

PubMed

Thimmaiah, Tim; Voje, William E; Carothers, James M

2015-01-01

With progress toward inexpensive, large-scale DNA assembly, the demand for simulation tools that allow the rapid construction of synthetic biological devices with predictable behaviors continues to increase. By combining engineered transcript components, such as ribosome binding sites, transcriptional terminators, ligand-binding aptamers, catalytic ribozymes, and aptamer-controlled ribozymes (aptazymes), gene expression in bacteria can be fine-tuned, with many corollaries and applications in yeast and mammalian cells. The successful design of genetic constructs that implement these kinds of RNA-based control mechanisms requires modeling and analyzing kinetically determined co-transcriptional folding pathways. Transcript design methods using stochastic kinetic folding simulations to search spacer sequence libraries for motifs enabling the assembly of RNA component parts into static ribozyme- and dynamic aptazyme-regulated expression devices with quantitatively predictable functions (rREDs and aREDs, respectively) have been described (Carothers et al., Science 334:1716-1719, 2011). Here, we provide a detailed practical procedure for computational transcript design by illustrating a high throughput, multiprocessor approach for evaluating spacer sequences and generating functional rREDs. This chapter is written as a tutorial, complete with pseudo-code and step-by-step instructions for setting up a computational cluster with an Amazon, Inc. web server and performing the large numbers of kinefold-based stochastic kinetic co-transcriptional folding simulations needed to design functional rREDs and aREDs. The method described here should be broadly applicable for designing and analyzing a variety of synthetic RNA parts, devices and transcripts.

Causative Role of Grapevine Red Blotch Virus in Red Blotch Disease.

PubMed

Yepes, Luz Marcela; Cieniewicz, Elizabeth; Krenz, Björn; McLane, Heather; Thompson, Jeremy R; Perry, Keith Lloyd; Fuchs, Marc

2018-05-17

Grapevine red blotch virus (GRBV) has a monopartite single-stranded DNA genome and is the type species of the genus Grablovirus in the family Geminiviridae. To address the etiological role of GRBV in the recently recognized red blotch disease of grapevine, infectious GRBV clones were engineered from the genome of each of the two previously identified phylogenetic clades for Agrobacterium tumefaciens-mediated inoculations of tissue culture-grown Vitis spp. plants. Following agroinoculation and one or two dormancy cycles, systemic GRBV infection was detected by multiplex polymerase chain reaction (PCR) in Vitis vinifera exhibiting foliar disease symptoms but not in asymptomatic vines. Infected rootstock genotype SO4 (V. berlandieri × V. riparia) exhibited leaf chlorosis and cupping, while infection was asymptomatic in agroinoculated 110R (V. berlandieri × V. rupestris), 3309C (V. riparia × V. rupestris), and V. rupestris. Spliced GRBV transcripts of the replicase-associated protein coding region accumulated in leaves of agroinfected vines, as shown by reverse-transcription PCR; this was consistent with systemic infection resulting from virus replication. Additionally, a virus progeny identical in nucleotide sequence to the infectious GRBV clones was recovered from agroinfected vines by rolling circle amplification, cloning, and sequencing. Concomitantly, subjecting naturally infected grapevines to microshoot tip culture resulted in an asymptomatic plant progeny that tested negative for GRBV in multiplex PCR. Altogether, our agroinoculation and therapeutic experiments fulfilled Koch's postulates and revealed the causative role of GRBV in red blotch disease.

Cirrus Horizontal Heterogeneity Effects on Cloud Optical Properties Retrieved from MODIS VNIR to TIR Channels as a Function of the Spatial Resolution

NASA Astrophysics Data System (ADS)

Fauchez, T.; Platnick, S. E.; Sourdeval, O.; Wang, C.; Meyer, K.; Cornet, C.; Szczap, F.

2017-12-01

Cirrus are an important part of the Earth radiation budget but an assessment of their role yet remains highly uncertain. Cirrus optical properties such as Cloud Optical Thickness (COT) and ice crystal effective particle size (Re) are often retrieved with a combination of Visible/Near InfraRed (VNIR) and ShortWave-InfraRed (SWIR) reflectance channels. Alternatively, Thermal InfraRed (TIR) techniques, such as the Split Window Technique (SWT), have demonstrated better sensitivity to thin cirrus. However, current satellite operational products for both retrieval methods assume that cloudy pixels are horizontally homogeneous (Plane Parallel and Homogeneous Approximation (PPHA)) and independent (Independent Pixel Approximation (IPA)). The impact of these approximations on cirrus retrievals needs to be understood and, as far as possible, corrected. Horizontal heterogeneity effects can be more easily estimated and corrected in the TIR range because they are mainly dominated by the PPA bias, which primarily depends on the COT subpixel heterogeneity. For solar reflectance channels, in addition to the PPHA bias, the IPA can lead to significant retrieval errors if there is large photon transport between cloudy columns in addition to brightening and shadowing effects that are more difficult to quantify.The effects of cirrus horizontal heterogeneity are here studied on COT and Re retrievals obtained using simulated MODIS reflectances at 0.86 and 2.11 μm and radiances at 8.5, 11.0 and 12.0 μm, for spatial resolutions ranging from 50 m to 10 km. For each spatial resolution, simulated TOA reflectances and radiances are combined for cloud optical property retrievals with a research-level optimal estimation retrieval method (OEM). The impact of horizontal heterogeneity on the retrieved products is assessed for different solar geometries and various combinations of the five channels.

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment

PubMed Central

Röthig, Till; Yum, Lauren K.; Kremb, Stephan G.; Roik, Anna; Voolstra, Christian R.

2017-01-01

Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L−1) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment. PMID:28303925

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment.

PubMed

Röthig, Till; Yum, Lauren K; Kremb, Stephan G; Roik, Anna; Voolstra, Christian R

2017-03-17

Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L -1 ) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment.

Detecting long tandem duplications in genomic sequences.

PubMed

Audemard, Eric; Schiex, Thomas; Faraut, Thomas

2012-05-08

Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,(a) we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS  <  1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations.

A recurrent deletion mutation in OPA1 causes autosomal dominant optic atrophy in a Chinese family

NASA Astrophysics Data System (ADS)

Zhang, Liping; Shi, Wei; Song, Liming; Zhang, Xiao; Cheng, Lulu; Wang, Yanfang; Ge, Xianglian; Li, Wei; Zhang, Wei; Min, Qingjie; Jin, Zi-Bing; Qu, Jia; Gu, Feng

2014-11-01

Autosomal dominant optic atrophy (ADOA) is the most frequent form of hereditary optic neuropathy and occurs due to the degeneration of the retinal ganglion cells. To identify the genetic defect in a family with putative ADOA, we performed capture next generation sequencing (CNGS) to screen known retinal disease genes. However, six exons failed to be sequenced by CNGS in optic atrophy 1 gene (OPA1). Sequencing of those exons identified a 4 bp deletion mutation (c.2983-1_2985del) in OPA1. Furthermore, we sequenced the transcripts of OPA1 from the patient skin fibroblasts and found there is six-nucleotide deletion (c.2984-c.2989, AGAAAG). Quantitative-PCR and Western blotting showed that OPA1 mRNA and its protein expression have no obvious difference between patient skin fibroblast and control. The analysis of protein structure by molecular modeling suggests that the mutation may change the structure of OPA1 by formation of an alpha helix protruding into an existing pocket. Taken together, we identified an OPA1 mutation in a family with ADOA by filling the missing CNGS data. We also showed that this mutation affects the structural intactness of OPA1. It provides molecular insights for clinical genetic diagnosis and treatment of optic atrophy.

A recurrent deletion mutation in OPA1 causes autosomal dominant optic atrophy in a Chinese family.

PubMed

Zhang, Liping; Shi, Wei; Song, Liming; Zhang, Xiao; Cheng, Lulu; Wang, Yanfang; Ge, Xianglian; Li, Wei; Zhang, Wei; Min, Qingjie; Jin, Zi-Bing; Qu, Jia; Gu, Feng

2014-11-06

Autosomal dominant optic atrophy (ADOA) is the most frequent form of hereditary optic neuropathy and occurs due to the degeneration of the retinal ganglion cells. To identify the genetic defect in a family with putative ADOA, we performed capture next generation sequencing (CNGS) to screen known retinal disease genes. However, six exons failed to be sequenced by CNGS in optic atrophy 1 gene (OPA1). Sequencing of those exons identified a 4 bp deletion mutation (c.2983-1_2985del) in OPA1. Furthermore, we sequenced the transcripts of OPA1 from the patient skin fibroblasts and found there is six-nucleotide deletion (c.2984-c.2989, AGAAAG). Quantitative-PCR and Western blotting showed that OPA1 mRNA and its protein expression have no obvious difference between patient skin fibroblast and control. The analysis of protein structure by molecular modeling suggests that the mutation may change the structure of OPA1 by formation of an alpha helix protruding into an existing pocket. Taken together, we identified an OPA1 mutation in a family with ADOA by filling the missing CNGS data. We also showed that this mutation affects the structural intactness of OPA1. It provides molecular insights for clinical genetic diagnosis and treatment of optic atrophy.

Molecular delineation of the Agave Red Worm Comadia redtenbacheri  (Lepidoptera: Cossidae).

PubMed

CÁrdenas-Aquino, MarÍa Del Rosario; AlarcÓn-rodrÍguez, Norma Marina; Rivas-Medrano, Mario; GonzÁlez-hernÁndez, HÉctor; Vargas-hernÁndez, Mateo; SÁnchez-Arroyo, Hussein; Llanderal-cÁzares, Celina

2018-01-25

Comadia redtenbacheri (Hammerschmidt) (Agave Red Worm) is the only member of the family Cossidae that has been described as a phytophagous specialist of the plant genus Agave, which is mainly distributed in México. A new extraction protocol adapted from Stewart Via (1993) has been implemented for sequencing the COI gene from samples collected in five states of the North Central (Querétaro and Zacatecas), South Central (Estado de México) and East Central (Hidalgo and Tlaxcala) regions of México with the purpose of contributing to delineation of the species. A Maximum Likelihood (ML) tree based on these COI sequences as well as COI sequences from other Cossinae species was developed to complement the existing morphological and taxonomic approaches to delineation of this species. As expected, our Comadia samples cluster together within a monophyletic clade that includes four C. redtenbacheri sequences previously reported. This group seems to be consistent with our reconstruction, which is supported by a bootstrap value of over 99%. The closely related branches associated with the latter group include organisms known to be the plant and tree borers of the Cossinae subfamily. The COI sequences from our samples were analyzed to determine the percentage of identity among the C. redtenbacheri in a first attempt to detect differences in the sequence that matches a particular region of México.

Optical layout and mechanical structure of polarimeter-interferometer system for Experimental Advanced Superconducting Tokamak

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

Zou, Z. Y.; Liu, H. Q., E-mail: hqliu@ipp.ac.cn; Jie, Y. X.

A Far-InfaRed (FIR) three-wave POlarimeter-INTerferometer (POINT) system for measurement current density profile and electron density profile is under development for the EAST tokamak. The FIR beams are transmitted from the laser room to the optical tower adjacent to EAST via ∼20 m overmoded dielectric waveguide and then divided into 5 horizontal chords. The optical arrangement was designed using ZEMAX, which provides information on the beam spot size and energy distribution throughout the optical system. ZEMAX calculations used to optimize the optical layout design are combined with the mechanical design from CATIA, providing a 3D visualization of the entire POINT system.

Optical layout and mechanical structure of polarimeter-interferometer system for Experimental Advanced Superconducting Tokamak.

PubMed

Zou, Z Y; Liu, H Q; Jie, Y X; Ding, W X; Brower, D L; Wang, Z X; Shen, J S; An, Z H; Yang, Y; Zeng, L; Wei, X C; Li, G S; Zhu, X; Lan, T

2014-11-01

A Far-InfaRed (FIR) three-wave POlarimeter-INTerferometer (POINT) system for measurement current density profile and electron density profile is under development for the EAST tokamak. The FIR beams are transmitted from the laser room to the optical tower adjacent to EAST via ∼20 m overmoded dielectric waveguide and then divided into 5 horizontal chords. The optical arrangement was designed using ZEMAX, which provides information on the beam spot size and energy distribution throughout the optical system. ZEMAX calculations used to optimize the optical layout design are combined with the mechanical design from CATIA, providing a 3D visualization of the entire POINT system.

Influence of Flow Sequencing Attributed to Climate Change and Climate Variability on the Assessment of Water-dependent Ecosystem Outcomes

NASA Astrophysics Data System (ADS)

Wang, J.; Nathan, R.; Horne, A.

2017-12-01

Traditional approaches to characterize water-dependent ecosystem outcomes in response to flow have been based on time-averaged hydrological indicators, however there is increasing recognition for the need to characterize ecological processes that are highly dependent on the sequencing of flow conditions (i.e. floods and droughts). This study considers the representation of flow regimes when considering assessment of ecological outcomes, and in particular, the need to account for sequencing and variability of flow. We conducted two case studies - one in the largely unregulated Ovens River catchment and one in the highly regulated Murray River catchment (both located in south-eastern Australia) - to explore the importance of flow sequencing to the condition of a typical long-lived ecological asset in Australia, the River Red Gum forests. In the first, the Ovens River case study, the implications of representing climate change using different downscaling methods (annual scaling, monthly scaling, quantile mapping, and weather generator method) on the sequencing of flows and resulting ecological outcomes were considered. In the second, the Murray River catchment, sequencing within a historic drought period was considered by systematically making modest adjustments on an annual basis to the hydrological records. In both cases, the condition of River Red Gum forests was assessed using an ecological model that incorporates transitions between ecological conditions in response to sequences of required flow components. The results of both studies show the importance of considering how hydrological alterations are represented when assessing ecological outcomes. The Ovens case study showed that there is significant variation in the predicted ecological outcomes when different downscaling techniques are applied. Similarly, the analysis in the Murray case study showed that the drought as it historically occurred provided one of the best possible outcomes for River Red Gum forests when compared to other re-arrangements of flow within the same drought. These results have implications for the way we represent climate change impacts and drought risk assessments where ecological outcomes are a key management objective.

Diurnal and Directional Responses of Chlorophyll Fluorescence and the PRI in a Cornfield

NASA Technical Reports Server (NTRS)

Middleton, Elizabeth; Cheng, Y. B.; Corp, L.; Campbell, P.; Kustas, W.

2010-01-01

Determining the health and vigor of vegetation using high spectral resolution remote sensing is an important goal which has application to monitoring agriculture and ecosystem productivity and carbon exchange. Two spectral indices used to assess whether vegetation is performing near-optimally or exhibiting symptoms of environmental stress (e.g., drought or nutrient deficiency, non-optimal temperatures, etc.) are the Photochemical Reflectance Index (PRI) and solar-induced red and far-red Chlorophyll Fluorescence (Fs). Both the PRI and Fs capture the dynamics of photoprotection mechanisms within green foliage: the PRI is based on the association of the reflected radiation in the green spectrum with the xanthophyll cycle, whereas Fs measures the emitted radiation in the red and far-red spectrum. Fs was determined from retrievals in the atmospheric oxygen absorption features centered at 688 and 760 nm using a modified Fraunhofer Line Depth (FLD) method. We previously demonstrated diurnal and seasonal PRI differences for sunlit vs. shaded foliage in a conifer forest canopy, as expressed in the hotspot and darkspot of the Bidirectional Reflectance Function (BRF). In a USDA-ARS experimental field site located in Beltsville, MD, USA, measurements were acquired over a corn crop from a nadir view in 2008 with an ASD FieldSpec Pro (Analytical Spectral Devices, Inc., Boulder, CO, USA) to study the behavior of the PRI for sunlit and shaded foliage as captured in reflectance variations associated with the BRF, in a I m tall canopy in the vegetative growth stage. Those observations were compared to simulations obtained from two radiative transfer models. Measurements were then acquired to examine whether the PRI and Fs were influenced by view zenith and azimuth geometries at different times of day. Those measurements were made in 2010 with the Ocean Optics USB4000 Miniature Fiber Optic Spectrometer (Ocean Optics Inc., Dunedin, Florida, USA) at several times during the day on multiple days throughout the growing season. We found that the PRI consistently had higher values, indicating lower stress, in the BRF darkspot associated with shaded foliage than in the hotspot associated with sunlit foliage. We also found that Fs exhibited differences associated with sunlit and shaded canopy sectors, which were most pronounced for the red/far-red Fs ratio. Values indicated greater physiological stress in afternoons compared to mornings, and in the early senescent canopy as compared to the vegetative growth stage, BRFs for both the PRI and the red/far-red Fs ratio were bowl-shaped for the full azimuth sweep of the canopy. These two spectral indices (PRI, Fs ratio) provided complementary information on the photosynthetic function of the corn canopy.

Single-Slit Diffraction: Transitioning from Geometric Optics to the Fraunhofer Regime

ERIC Educational Resources Information Center

Panuski, Christopher L.; Mungan, Carl E.

2016-01-01

Suppose a red laser beam (of wavelength ? equal to 0.660 µm) is expanded using an optical telescope into a collimated, approximately plane wave that is 5.68 mm in diameter. Pass that beam through a tall rectangular slit whose width "a" is gradually reduced from 3.30 to 0.100 mm. Look at its image on a screen located at a distance…

Microscopic Optical Characterization of ZnO Bulk Crystals, Free Standing III-Nitride Substrates and III-V Structures for Non-Linear Optics

DTIC Science & Technology

2008-10-01

concentration (M.R. Phillips, M.Wagner, O.Gelhausen, V.Coleman, J.B. Brady, C. Jagadish, E. Malguth, A. Hoffmann, E.M. Goldys , J.J. Rusell; E.MRS...Malguth, A. Hoffmann, E.M. Goldys , J.J. Rusell; E.MRS Fall meeting, Symp. F, (Warsaw, Poland, 2004)); it suggests that the shift towards the red of

Companions to α Orionis

NASA Astrophysics Data System (ADS)

Karovska, M.; Nisenson, P.; Noyes, R. W.; Stachnik, R.

Detection of two close optical companions to the red supergiant a Ori was accomplished using the PAPA detector for data recording, and speckle imaging for image reconstruction. Our analysis favors an interpretation in which the two optical sources are stellar companions to a Ori.The observed time dependent variations of the polarization of a Ori can be interpreted as being due to a systemic asymmetry created by one of the companions.

Au nanoparticle monolayers covered with sol-gel oxide thin films: optical and morphological study.

PubMed

Della Gaspera, Enrico; Karg, Matthias; Baldauf, Julia; Jasieniak, Jacek; Maggioni, Gianluigi; Martucci, Alessandro

2011-11-15

In this work, we provide a detailed study of the influence of thermal annealing on submonolayer Au nanoparticle deposited on functionalized surfaces as standalone films and those that are coated with sol-gel NiO and TiO(2) thin films. The systems are characterized through the use of UV-vis absorption, X-ray diffraction (XRD), atomic force microscopy (AFM), scanning electron microscopy (SEM), and spectroscopic ellipsometry. The surface plasmon resonance peak of the Au nanoparticles was found to red-shift and increase in intensity with increasing surface coverage, an observation that is directly correlated to the complex refractive index properties of Au nanoparticle layers. The standalone Au nanoparticles sinter at 200 °C, and a relationship between the optical properties and the annealing temperature is presented. When overcoated with sol-gel metal oxide films (NiO, TiO(2)), the optical properties of the Au nanoparticles are strongly affected by the metal oxide, resulting in an intense red shift and broadening of the plasmon band; moreover, the temperature-driven sintering is strongly limited by the metal oxide layer. Optical sensing tests for ethanol vapor are presented as one possible application, showing reversible sensing dynamics and confirming the effect of Au nanoparticles in increasing the sensitivity and in providing a wavelength dependent response, thus confirming the potential use of such materials as optical probes.

Optical properties of natural dyes on the dye-sensitized solar cells (DSSC) performance

NASA Astrophysics Data System (ADS)

Pratiwi, D. D.; Nurosyid, F.; Supriyanto, A.; Suryana, R.

2016-11-01

This study reported several natural dyes for application in dye-sensitized solar cells (DSSC). This study aims was to determine the effect of optical absorption properties of natural dyes on efficiency of DSSC. The sandwich structure of DSSC consist of TiO2 as working electrode, carbon layer as counter electrode, natural dyes as photosensitizer, and electrolyte as electron transfer media. The natural dyes used in this experiment were extracted from dragon fruit anthocyanin, mangosteen peels anthocyanin, and red cabbage anthocyanin. The absorbance of dyes solutions and the adsorption of the dye on the surface of TiO2 were characterized using UV-Vis spectrophotometer, the quantum efficiency versus wavelength was characterized using incident photon-to-current efficiency (IPCE) measurement system, and the efficiency of DSSC was calculated using I-V meter. UV-Vis characteristic curves showed that wavelength absorption of anthocyanin dye of red cabbage was 450 - 580 nm, anthocyanin of mangosteen peels was 400 - 480 nm, and anthocyanin of dragon fruit was 400 - 650 nm. Absorption spectra of the dye adsorption on the surface of TiO2 which was resulted in the highest absorbance of red cabbage anthocyanin. IPCE characteristic curves with anthocyanin dye of red cabbage, mangosteen peels anthocyanin, and dragon fruit anthocyanin resulted quantum efficiency of 0.058%; 0.047%; and 0.043%, respectively at wavelength maximum about 430 nm. I-V characteristic curves with anthocyanin dye of red cabbage, mangosteen peels anthocyanin, and dragon fruit anthocyanin resulted efficiency of 0.054%; 0.042%; and 0.024%, respectively.

A semianalytical MERIS green-red band algorithm for identifying phytoplankton bloom types in the East China Sea

NASA Astrophysics Data System (ADS)

Tao, Bangyi; Mao, Zhihua; Lei, Hui; Pan, Delu; Bai, Yan; Zhu, Qiankun; Zhang, Zhenglong

2017-03-01

A new bio-optical algorithm based on the green and red bands of the Medium Resolution Imaging Spectrometer (MERIS) is developed to differentiate the harmful algal blooms of Prorocentrum donghaiense Lu (P. donghaiense) from diatom blooms in the East China Sea (ECS). Specifically, a novel green-red index (GRI), actually an indicator for a(510) of bloom waters, is retrieved from a semianalytical bio-optical model based on the green and red bands of phytoplankton-absorption and backscattering spectra. In addition, a MERIS-based diatom index (DIMERIS) is derived by adjusting a Moderate Resolution Imaging Spectroradiometer (MODIS) diatom index algorithm to the MERIS bands. Finally, bloom types are effectively differentiated in the feature spaces of the green-red index and DIMERIS. Compared with three previous MERIS-based quasi-analytical algorithm (QAA) algorithms and three existing classification methods, the proposed GRI and classification method have the best discrimination performance when using the MERIS data. Further validations of the algorithm by using several MERIS image series and near-concurrent in situ observations indicate that our algorithm yields the best classification accuracy and thus can be used to reliably detect and classify P. donghaiense and diatom blooms in the ECS. This is the first time that the MERIS data have been used to identify bloom types in the ECS. Our algorithm can also be used for the successor of the MERIS, the Ocean and Land Color Instrument, which will aid the long-term observation of species succession in the ECS.

Multichannel optical sensing device

DOEpatents

Selkowitz, S.E.

1985-08-16

A multichannel optical sensing device is disclosed, for measuring the outdoor sky luminance or illuminance or the luminance or illuminance distribution in a room, comprising a plurality of light receptors, an optical shutter matrix including a plurality of liquid crystal optical shutter elements operable by electrical control signals between light transmitting and light stopping conditions, fiber optical elements connected between the receptors and the shutter elements, a microprocessor based programmable control unit for selectively supplying control signals to the optical shutter elements in a programmable sequence, a photodetector including an optical integrating spherical chamber having an input port for receiving the light from the shutter matrix and at least one detector element in the spherical chamber for producing output signals corresponding to the light, and output units for utilizing the output signals including a storage unit having a control connection to the microprocessor based programmable control unit for storing the output signals under the sequence control of the programmable control unit.

Multichannel optical sensing device

DOEpatents

Selkowitz, Stephen E.

1990-01-01

A multichannel optical sensing device is disclosed, for measuring the outr sky luminance or illuminance or the luminance or illuminance distribution in a room, comprising a plurality of light receptors, an optical shutter matrix including a plurality of liquid crystal optical shutter elements operable by electrical control signals between light transmitting and light stopping conditions, fiber optic elements connected between the receptors and the shutter elements, a microprocessor based programmable control unit for selectively supplying control signals to the optical shutter elements in a programmable sequence, a photodetector including an optical integrating spherical chamber having an input port for receiving the light from the shutter matrix and at least one detector element in the spherical chamber for producing output signals corresponding to the light, and output units for utilizing the output signals including a storage unit having a control connection to the microprocessor based programmable control unit for storing the output signals under the sequence control of the programmable control unit.

RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.

PubMed

Sun, Yongmei; Li, Xing; Wu, Di; Pan, Qi; Ji, Yuefeng; Ren, Hong; Ding, Keyue

2016-01-01

RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software - 'RED' (RNA Editing sites Detector) - for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI). To improve performance, we used MySQL database management system (DBMS) for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75) but similar specificity (0.5). RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector.

Light-Induced Expression of a MYB Gene Regulates Anthocyanin Biosynthesis in Red Apples1

PubMed Central

Takos, Adam M.; Jaffé, Felix W.; Jacob, Steele R.; Bogs, Jochen; Robinson, Simon P.; Walker, Amanda R.

2006-01-01

Anthocyanins are secondary metabolites found in higher plants that contribute to the colors of flowers and fruits. In apples (Malus domestica Borkh.), several steps of the anthocyanin pathway are coordinately regulated, suggesting control by common transcription factors. A gene encoding an R2R3 MYB transcription factor was isolated from apple (cv Cripps' Pink) and designated MdMYB1. Analysis of the deduced amino acid sequence suggests that this gene encodes an ortholog of anthocyanin regulators in other plants. The expression of MdMYB1 in both Arabidopsis (Arabidopsis thaliana) plants and cultured grape cells induced the ectopic synthesis of anthocyanin. In the grape (Vitis vinifera) cells MdMYB1 stimulated transcription from the promoters of two apple genes encoding anthocyanin biosynthetic enzymes. In ripening apple fruit the transcription of MdMYB1 was correlated with anthocyanin synthesis in red skin sectors of fruit. When dark-grown fruit were exposed to sunlight, MdMYB1 transcript levels increased over several days, correlating with anthocyanin synthesis in the skin. MdMYB1 gene transcripts were more abundant in red skin apple cultivars compared to non-red skin cultivars. Several polymorphisms were identified in the promoter of MdMYB1. A derived cleaved amplified polymorphic sequence marker designed to one of these polymorphisms segregated with the inheritance of skin color in progeny from a cross of an unnamed red skin selection (a sibling of Cripps' Pink) and the non-red skin cultivar Golden Delicious. We conclude that MdMYB1 coordinately regulates genes in the anthocyanin pathway and the expression level of this regulator is the genetic basis for apple skin color. PMID:17012405

Ultrafast transient absorption revisited: Phase-flips, spectral fingers, and other dynamical features

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

Cina, Jeffrey A., E-mail: cina@uoregon.edu; Kovac, Philip A.; Jumper, Chanelle C.

We rebuild the theory of ultrafast transient-absorption/transmission spectroscopy starting from the optical response of an individual molecule to incident femtosecond pump and probe pulses. The resulting description makes use of pulse propagators and free molecular evolution operators to arrive at compact expressions for the several contributions to a transient-absorption signal. In this alternative description, which is physically equivalent to the conventional response-function formalism, these signal contributions are conveniently expressed as quantum mechanical overlaps between nuclear wave packets that have undergone different sequences of pulse-driven optical transitions and time-evolution on different electronic potential-energy surfaces. Using this setup in application to amore » simple, multimode model of the light-harvesting chromophores of PC577, we develop wave-packet pictures of certain generic features of ultrafast transient-absorption signals related to the probed-frequency dependence of vibrational quantum beats. These include a Stokes-shifting node at the time-evolving peak emission frequency, antiphasing between vibrational oscillations on opposite sides (i.e., to the red or blue) of this node, and spectral fingering due to vibrational overtones and combinations. Our calculations make a vibrationally abrupt approximation for the incident pump and probe pulses, but properly account for temporal pulse overlap and signal turn-on, rather than neglecting pulse overlap or assuming delta-function excitations, as are sometimes done.« less

The identification of post-starburst galaxies at z ˜ 1 using multiwavelength photometry: a spectroscopic verification

NASA Astrophysics Data System (ADS)

Maltby, David T.; Almaini, Omar; Wild, Vivienne; Hatch, Nina A.; Hartley, William G.; Simpson, Chris; McLure, Ross J.; Dunlop, James; Rowlands, Kate; Cirasuolo, Michele

2016-06-01

Despite decades of study, we still do not fully understand why some massive galaxies abruptly switch off their star formation in the early Universe, and what causes their rapid transition to the red sequence. Post-starburst galaxies provide a rare opportunity to study this transition phase, but few have currently been spectroscopically identified at high redshift (z > 1). In this paper, we present the spectroscopic verification of a new photometric technique to identify post-starbursts in high-redshift surveys. The method classifies the broad-band optical-near-infrared spectral energy distributions (SEDs) of galaxies using three spectral shape parameters (supercolours), derived from a principal component analysis of model SEDs. When applied to the multiwavelength photometric data in the UKIDSS Ultra Deep Survey, this technique identified over 900 candidate post-starbursts at redshifts 0.5 < z < 2.0. In this study, we present deep optical spectroscopy for a subset of these galaxies, in order to confirm their post-starburst nature. Where a spectroscopic assessment was possible, we find the majority (19/24 galaxies; ˜80 per cent) exhibit the strong Balmer absorption (H δ equivalent width Wλ > 5 Å) and Balmer break, characteristic of post-starburst galaxies. We conclude that photometric methods can be used to select large samples of recently-quenched galaxies in the distant Universe.

Cascade synthesis of a gold nanoparticle-network polymer composite

DOE PAGES

Grubjesic, Simonida; Ringstrand, Bryan Scott; Jungjohann, Katherine L.; ...

2015-11-02

In this paper, the multi-step, cascade synthesis of a self-supporting, hierarchically-structured gold nanoparticle hydrogel composite is described. The composite is spontaneously prepared from a non-covalent, lamellar lyotropic mesophase composed of amphiphiles that support the reactive constituents, a mixture of hydroxyl- and acrylate-end-derivatized PEO 117-PPO 47-PEO 117 and [AuCl 4] -. The reaction sequence begins with the auto-reduction of aqueous [AuCl 4] - by PEO 117-PPO 47-PEO 117 which leads to both the production of Au NPs and the free radical initiated polymerization and crosslinking of the acrylate endderivatized PEO 117-PPO 47-PEO 117 to yield a network polymer. Optical spectroscopy andmore » TEM monitored the reduction of [AuCl 4] -, formation of large aggregated Au NPs and oxidative etching into a final state of dispersed, spherical Au NPs. ATR/FT-IR spectroscopy and thermal analysis confirms acrylate crosslinking to yield the polymer network. X-ray scattering (SAXS and WAXS) monitored the evolution of the multilamellar structured mesophase and revealed the presence of semi-crystalline PEO confined within the water layers. The hydrogel could be reversibly swollen without loss of the well-entrained Au NPs with full recovery of composite structure. Finally, optical spectroscopy shows a notable red shift (Δλ~ 45 nm) in the surface plasmon resonance between swollen and contracted states, demonstrating solvent-mediated modulation of the internal NP packing arrangement.« less

Binding of nucleotides by T4 DNA ligase and T4 RNA ligase: optical absorbance and fluorescence studies.

PubMed Central

Cherepanov, A V; de Vries, S

2001-01-01

The interaction of nucleotides with T4 DNA and RNA ligases has been characterized using ultraviolet visible (UV-VIS) absorbance and fluorescence spectroscopy. Both enzymes bind nucleotides with the K(d) between 0.1 and 20 microM. Nucleotide binding results in a decrease of absorbance at 260 nm due to pi-stacking with an aromatic residue, possibly phenylalanine, and causes red-shifting of the absorbance maximum due to hydrogen bonding with the exocyclic amino group. T4 DNA ligase is shown to have, besides the catalytic ATP binding site, another noncovalent nucleotide binding site. ATP bound there alters the pi-stacking of the nucleotide in the catalytic site, increasing its optical extinction. The K(d) for the noncovalent site is approximately 1000-fold higher than for the catalytic site. Nucleotides quench the protein fluorescence showing that a tryptophan residue is located in the active site of the ligase. The decrease of absorbance around 298 nm suggests that the hydrogen bonding interactions of this tryptophan residue are weakened in the ligase-nucleotide complex. The excitation/emission properties of T4 RNA ligase indicate that its ATP binding pocket is in contact with solvent, which is excluded upon binding of the nucleotide. Overall, the spectroscopic analysis reveals important similarities between T4 ligases and related nucleotidyltransferases, despite the low sequence similarity. PMID:11721015

Peruvian Maca (Lepidium peruvianum) - III: The Effects of Cultivation Altitude on Phytochemical and Genetic Differences in the Four Prime Maca Phenotypes.

PubMed

Meissner, Henry O; Mscisz, Alina; Baraniak, Marek; Piatkowska, Ewa; Pisulewski, Pawel; Mrozikiewicz, Mieczyslaw; Bobkiewicz-Kozlowska, Teresa

2017-06-01

In two trials, dietary and Glucosinolates' characteristics in four Maca phenotypes have been examined with an extension into the determination of DNA sequences. Hypocotyls of the four prime phenotypes of Peruvian Maca - Lepidium peruvianum Chacon, labelled as "Yellow", "Black", "Red" and "Purple" were separated from mixed Maca crops cultivated in four geographically-distant locations in the Peruvian Andes at altitudes between 2,800m and 4,300 m a.s.l. It was found that at higher altitudes where Red and Purple Maca phenotypes were grown, the significantly higher ( P <0.05) Glucosinolates' concentrations, adopted as the marker of Maca physiological activity, were observed with the Purple phenotype showing the highest Glucosinolates' content at 4,300m a.s.l., followed by the Red-coloured hypocotyls. Black Maca showed a reversal, but also a significant ( P <0.05) trend, while the Yellow phenotype showed no visible altitude-inflicted response ( P >0.05) and has consistently the lowest Glucosinolates content. Thus, it is reasonable to assume that the altitude at which Red, Purple and Black phenotypes of L. peruvianum are grown, may be responsible for the variation in physiologic functionalities, leading to different than expected specific therapeutic and health benefits induced by Maca phenotypes grown at diverse altitudes. Although promising, insufficiently precise differences in DNA sequences failed to distinguish, without any reasonable doubt, four Maca phenotypes cultivated either in the same or geographically-distant locations, and harvested at different altitudes a.s.l. Further research on DNA sequences is needed, with more primers and larger number of Maca phenotypes, considering biosynthesis of secondary metabolites and adaptation pathways induced by harsh environment at altitudes where Maca is cultivated.

Mantle flow beneath Arabia offset from the opening Red Sea

NASA Astrophysics Data System (ADS)

Chang, Sung-Joon; Merino, Miguel; Van der Lee, Suzan; Stein, Seth; Stein, Carol A.

2011-02-01

Continental rifting involves a poorly understood sequence of lithospheric stretching, volcanism, and mantle flow that evolves to seafloor spreading. We present new insight from inversion of seismic traveltimes and waveforms beneath Arabia and surroundings. Low velocities occur beneath the southern Red Sea and Gulf of Aden, consistent with active spreading. However, hot material extends not below the northern Red Sea, but is offset eastward beneath Arabia, showing mantle flow from the Afar hotspot. The location of this channel beneath volcanic rocks erupted since rifting began 30 million years ago indicates that flow moves with Arabia. We propose that the absence of seafloor spreading in the northern Red Sea reflects the offset flow. This geometry may evolve to spreading in the Northern Red Sea, rifting of Arabia, or both. This situation has aspects of both active and passive rifting, showing that both can occur before coalescing to seafloor spreading.

Signal Statistics and Maximum Likelihood Sequence Estimation in Intensity Modulated Fiber Optic Links Containing a Single Optical Pre-amplifier.

PubMed

Alić, Nikola; Papen, George; Saperstein, Robert; Milstein, Laurence; Fainman, Yeshaiahu

2005-06-13

Exact signal statistics for fiber-optic links containing a single optical pre-amplifier are calculated and applied to sequence estimation for electronic dispersion compensation. The performance is evaluated and compared with results based on the approximate chi-square statistics. We show that detection in existing systems based on exact statistics can be improved relative to using a chi-square distribution for realistic filter shapes. In contrast, for high-spectral efficiency systems the difference between the two approaches diminishes, and performance tends to be less dependent on the exact shape of the filter used.

Development of a drug assay using surface-enhanced Raman spectroscopy

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

Angel, S.M.; Roe, J.N.; Andresen, B.D.

1990-05-01

Surface-enhanced Raman spectroscopy has been used to detect low levels of several chemical compounds, including the drugs of abuse -- cocaine hydrochloride and methamphetamine hydrochloride. Raman spectra of these substances have also been taken over optical fibers using red-wavelength excitation. These measurements demonstrate the feasibility of the remote red-wavelength excitation. These measurements demonstrate the feasibility of the remote determination of various target chemicals using diode excitation and diode array detection. 5 refs., 5 figs.

Status of the JWST Science Instrument Payload

NASA Technical Reports Server (NTRS)

Greenhouse, Matt

2016-01-01

The James Webb Space Telescope (JWST) Integrated Science Instrument Module (ISIM) system consists of five sensors (4 science): Mid-Infrared Instrument (MIRI), Near Infrared Imager and Slitless Spectrograph (NIRISS), Fine Guidance Sensor (FGS), Near InfraRed Camera (NIRCam), Near InfraRed Spectrograph (NIRSpec); and nine instrument support systems: Optical metering structure system, Electrical Harness System; Harness Radiator System, ISIM Electronics Compartment, ISIM Remote Services Unit, Cryogenic Thermal Control System, Command and Data Handling System, Flight Software System, Operations Scripts System.

Calcium Sensitive Fluorescent Dyes Fluo-4 and Fura Red under Pressure: Behaviour of Fluorescence and Buffer Properties under Hydrostatic Pressures up to 200 MPa.

PubMed

Schneidereit, D; Vass, H; Reischl, B; Allen, R J; Friedrich, O

2016-01-01

The fluorescent Ca2+ sensitive dyes Fura Red (ratiometric) and Fluo-4 (non-ratiometric) are widely utilized for the optical assessment of Ca2+ fluctuations in vitro as well as in situ. The fluorescent behavior of these dyes is strongly depends on temperature, pH, ionic strength and pressure. It is crucial to understand the response of these dyes to pressure when applying calcium imaging technologies in the field of high pressure bioscience. Therefore, we use an optically accessible pressure vessel to pressurize physiological Ca2+-buffered solutions at different fixed concentrations of free Ca2+ (1 nM to 25.6 μM) and a specified dye concentration (12 μM) to pressures of 200 MPa, and record dye fluorescence intensity. Our results show that Fluo-4 fluorescence intensity is reduced by 31% per 100 MPa, the intensity of Fura Red is reduced by 10% per 100 MPa. The mean reaction volume for the dissociation of calcium from the dye molecules [Formula: see text] is determined to -17.8 ml mol-1 for Fluo-4 and -21.3 ml mol-1 for Fura Red. Additionally, a model is presented that is used to correct for pressure-dependent changes in pH and binding affinity of Ca2+ to EGTA, as well as to determine the influence of these changes on dye fluorescence.

2D photonic crystal layer assisted thiosilicate ceramic plate with red-emitting film for high quality w -LEDs

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

Dai, Wubin; Lei, Yifeng; Zhou, Jia

In this work, we have succeeded in obtaining high quality warm w-light-emitting-diodes (LEDs) by adopting hybrid two-dimensional (2D) structure of SiNx photonic crystal layer (PCL) assisted cyan-emitting ceramic-plate thiosilicate SrLa2Si2S8:Ce3+ with red-emitting film SrLiAl3N4:Eu2+ phosphor on a 430 nm blue LED chip at 350 mA. 2D SiNx PCL was capped with thiosilicate is because it can enhance the luminous efficacy and maintain the low correlated color temperature (CCT) and high color-rendering index (CRI). High luminous efficacy (82.3 lm/W), high special CRI (R9=75) as well as the low CCT (5431 K) of the optimal w-LED was obtained due to the assistancesmore » of 2D SiNx PCL and narrow-band red-emitting phosphor with the doping percentage at 10 wt%. The synthesis processes, structural analysis, optical properties and LED device performances were detailed investigated to find out the relationship between the optimum composition and good optical properties. Based on intriguing luminescence properties by the 2D SiNx PCL and red-emitting film phosphor introducing, we proclaim this method could also have high potential application in other phosphor-converted w-LEDs.« less

Meta-Analysis of the Detection of Plant Pigment Concentrations Using Hyperspectral Remotely Sensed Data

PubMed Central

Huang, Jingfeng; Wei, Chen; Zhang, Yao; Blackburn, George Alan; Wang, Xiuzhen; Wei, Chuanwen; Wang, Jing

2015-01-01

Passive optical hyperspectral remote sensing of plant pigments offers potential for understanding plant ecophysiological processes across a range of spatial scales. Following a number of decades of research in this field, this paper undertakes a systematic meta-analysis of 85 articles to determine whether passive optical hyperspectral remote sensing techniques are sufficiently well developed to quantify individual plant pigments, which operational solutions are available for wider plant science and the areas which now require greater focus. The findings indicate that predictive relationships are strong for all pigments at the leaf scale but these decrease and become more variable across pigment types at the canopy and landscape scales. At leaf scale it is clear that specific sets of optimal wavelengths can be recommended for operational methodologies: total chlorophyll and chlorophyll a quantification is based on reflectance in the green (550–560nm) and red edge (680–750nm) regions; chlorophyll b on the red, (630–660nm), red edge (670–710nm) and the near-infrared (800–810nm); carotenoids on the 500–580nm region; and anthocyanins on the green (550–560nm), red edge (700–710nm) and near-infrared (780–790nm). For total chlorophyll the optimal wavelengths are valid across canopy and landscape scales and there is some evidence that the same applies for chlorophyll a. PMID:26356842

Galactic Metropolis

NASA Image and Video Library

2013-12-18

The collection of red dots seen here show one of several very distant galaxy clusters discovered by combining ground-based optical data from the NOAO Kitt Peak National Observatory with infrared data from NASA Spitzer Space Telescope.

Joint estimation of motion and illumination change in a sequence of images

NASA Astrophysics Data System (ADS)

Koo, Ja-Keoung; Kim, Hyo-Hun; Hong, Byung-Woo

2015-09-01

We present an algorithm that simultaneously computes optical flow and estimates illumination change from an image sequence in a unified framework. We propose an energy functional consisting of conventional optical flow energy based on Horn-Schunck method and an additional constraint that is designed to compensate for illumination changes. Any undesirable illumination change that occurs in the imaging procedure in a sequence while the optical flow is being computed is considered a nuisance factor. In contrast to the conventional optical flow algorithm based on Horn-Schunck functional, which assumes the brightness constancy constraint, our algorithm is shown to be robust with respect to temporal illumination changes in the computation of optical flows. An efficient conjugate gradient descent technique is used in the optimization procedure as a numerical scheme. The experimental results obtained from the Middlebury benchmark dataset demonstrate the robustness and the effectiveness of our algorithm. In addition, comparative analysis of our algorithm and Horn-Schunck algorithm is performed on the additional test dataset that is constructed by applying a variety of synthetic bias fields to the original image sequences in the Middlebury benchmark dataset in order to demonstrate that our algorithm outperforms the Horn-Schunck algorithm. The superior performance of the proposed method is observed in terms of both qualitative visualizations and quantitative accuracy errors when compared to Horn-Schunck optical flow algorithm that easily yields poor results in the presence of small illumination changes leading to violation of the brightness constancy constraint.

First molecular detection and characterization of Marek's disease virus in red-crowned cranes (Grus japonensis): a case report.

PubMed

Lian, Xue; Ming, Xin; Xu, Jiarong; Cheng, Wangkun; Zhang, Xunhai; Chen, Hongjun; Ding, Chan; Jung, Yong-Sam; Qian, Yingjuan

2018-04-03

Marek's disease virus (MDV) resides in the genus Mardivirus in the family Herpesviridae. MDV is a highly contagious virus that can cause neurological lesions, lymphocytic proliferation, immune suppression, and death in avian species, including Galliformes (chickens, quails, partridges, and pheasants), Strigiformes (owls), Anseriformes (ducks, geese, and swans), and Falconiformes (kestrels). In 2015, two red-crowned cranes died in Nanjing (Jiangsu, China). It was determined that the birds were infected with Marek's disease virus by histopathological examination, polymerase chain reaction (PCR), gene sequencing and sequence analysis of tissue samples from two cranes. Gross lesions included diffuse nodules in the skin, muscle, liver, spleen, kidney, gizzard and heart, along with liver enlargement and gizzard mucosa hemorrhage. Histopathological assay showed that infiltrative lymphocytes and mitotic figures existed in liver and heart. The presence of MDV was confirmed by PCR. The sequence analysis of the Meq gene showed 100% identity with Md5, while the VP22 gene showed the highest homology with CVI988. Furthermore, the phylogenetic analysis of the VP22 and Meq genes suggested that the MDV (from cranes) belongs to MDV serotype 1. We describe the first molecular detection of Marek's disease in red-crowned cranes based on the findings previously described. To our knowledge, this is also the first molecular identification of Marek's disease virus in the order Gruiformes and represents detection of a novel MDV strain.

Effect of glucose on the optical properties of arterial blood using Mie theory simulations

NASA Astrophysics Data System (ADS)

Clancy, Neil T.; Leahy, Martin J.

2005-08-01

The glucose concentration in arterial plasma has immediate effects on the optical properties of blood-bearing tissue due primarily to the alteration of refractive index mismatch between the scattering particles (red blood cells) and the medium (plasma). The influence of these effects on pulse oximetry is investigated using a numerical model based on Mie theory. The objective is to determine whether or not physiological fluctuations in blood glucose levels could sufficiently vary the optical properties to shift the calibration curve of a commercial pulse oximeter significantly.

Optomechanical design of TMT NFIRAOS Subsystems at INO

NASA Astrophysics Data System (ADS)

Lamontagne, Frédéric; Desnoyers, Nichola; Grenier, Martin; Cottin, Pierre; Leclerc, Mélanie; Martin, Olivier; Buteau-Vaillancourt, Louis; Boucher, Marc-André; Nash, Reston; Lardière, Olivier; Andersen, David; Atwood, Jenny; Hill, Alexis; Byrnes, Peter W. G.; Herriot, Glen; Fitzsimmons, Joeleff; Véran, Jean-Pierre

2017-08-01

The adaptive optics system for the Thirty Meter Telescope (TMT) is the Narrow-Field InfraRed Adaptive Optics System (NFIRAOS). Recently, INO has been involved in the optomechanical design of several subsystems of NFIRAOS, including the Instrument Selection Mirror (ISM), the NFIRAOS Beamsplitters (NBS), and the NFIRAOS Source Simulator system (NSS) comprising the Focal Plane Mask (FPM), the Laser Guide Star (LGS) sources, and the Natural Guide Star (NGS) sources. This paper presents an overview of these subsystems and the optomechanical design approaches used to meet the optical performance requirements under environmental constraints.

Bistable optical devices with laser diodes coupled to absorbers of narrow spectral bandwidth.

PubMed

Maeda, Y

1994-06-20

An optical signal inverter was demonstrated with a combination of the following two effects: One is the decrease of the transmission of an Er-doped YAG crystal with increasing red shift of a laser diode resulting from an increase in the injection current, and the other is a negative nonlinear absorption in which the transmission decreases inversely with increasing laser intensity. Because a hysteresis characteristic exists in the relationship between the wavelength and the injection current of the laser diode, an optical bistability was observed in this system.

The dressed atom as binary phase modulator: towards attojoule/edge optical phase-shift keying.

PubMed

Kerckhoff, Joseph; Armen, Michael A; Pavlichin, Dmitri S; Mabuchi, Hideo

2011-03-28

We use a single 133Cs atom strongly coupled to an optical resonator to induce random binary phase modulation of a near infra-red, ∼ 500 pW laser beam, with each modulation edge caused by the dissipation of a single photon (≈ 0.23 aJ) by the atom. While our ability to deterministically induce phase edges with an additional optical control beam is limited thus far, theoretical analysis of an analogous, solid-state system indicates that efficient external control should be achievable in demonstrated nanophotonic systems.

A colorimetric turn-on optical chemosensor for Cu2+ ions and its application as solid state sensor

NASA Astrophysics Data System (ADS)

Pannipara, Mehboobali; Al-Sehemi, Abdullah G.; Assiri, Mohammed; Kalam, Abul

2018-05-01

We report a novel coumarin based optical chemosensor (Probe 1) for the selective and sensitive detection of Cu2+ ions in aqueous medium. The addition of Cu2+ ions to Probe 1 shows distinct color change from light yellow to pinkish red color under visible light with the sensing limit of 1.54 μM. Moreover, practical utility of Probe 1 as solid state optical sensor (test paper, TLC plates) for sensing Cu2+ has been demonstrated by instantaneous "naked eye" response.

Optical designs for MWIR and four quadrant detectors by using beam steering methods in missile applications

NASA Astrophysics Data System (ADS)

Sakarya, Doǧan Uǧur

2017-10-01

Beam steering optical arrangement needs less volume envelope for same field of regard than other gimbal approaches. Both for imaging and four quadrant missile applications, volume is critical parameter limiting system performance. Therefore, a conceptual design of beam steering method has been focused on both imaging and four quadrant missiles. In this study; four different optical designs have been made by using both beam steering and regular method for mid-wave infra-red imaging and four quadrant systems. Optical designs performances have been illustrated in simulation results. By using manufactured Risley prisms, some experimental results are conducted to compare simulations results.

Second harmonic generation by all-optical poling and its relaxation in the polymer films containing azo sulfonamide chromophores

NASA Astrophysics Data System (ADS)

Ortyl, E.; Chan, S. W.; Nunzi, J.-M.; Kucharski, S.

2006-11-01

Polyurethane polymers containing azo sulfonamide chromophores were obtained by coupling reaction of the precursor polyurethane with corresponding diazonium salts. The chromophores, showing high hyperpolarizability value on molecular scale, were found to undergo orientation by all-optical poling method yielding macroscopic nonlinear optical response. The rate of generation and decay of the second-order nonlinear susceptibility was evaluated as a function of time. It was established that the polymers containing sulfonamide type chromophores showed higher stability of the nonlinear optical signal as compared with those modified with a nitro-acceptor groups of the Disperse Red type.