Insights into Korean red fox (Vulpes vulpes) based on mitochondrial cytochrome b sequence variation in East Asia.

PubMed

Yu, Jeong-Nam; Han, Sang-Hoon; Kim, Bang-Hwan; Kryukov, Alexey P; Kim, Soonok; Lee, Byoung-Yoon; Kwak, Myounghai

2012-11-01

The red fox (Vulpes vulpes) is the most widely distributed terrestrial carnivore in the world, occurring throughout most of North America, Europe, Asia, and North Africa. In South Korea, however, this species has been drastically reduced due to habitat loss and poaching. Consequently, it is classified as an endangered species in Korea. As a first step of a planned red fox restoration project, preserved red fox museum specimens were used to determine the genetic status of red foxes that had previously inhabited South Korea against red foxes from neighboring countries. Total eighty three mtDNA cytochrome b sequences, including 22 newly obtained East Asian red fox sequences and worldwide red fox sequences from NCBI, were clustered into three clades (i.e., I, II, and III) based on haplotype network and neighbor-joining trees. The mean genetic distance between clades was 2.0%. Clade III contained South Korean and other East Asian samples in addition to Eurasian and North Pacific individuals. In clade III, South Korean individuals were separated into two lineages of Eurasian and North Pacific groups, showing unclear phylogeographic structuring and admixture. This suggests that South Korean red fox populations may have been composed of individuals from these two different genetic lineages.

Engineering an efficient and tight D-amino acid-inducible gene expression system in Rhodosporidium/Rhodotorula species.

PubMed

Liu, Yanbin; Koh, Chong Mei John; Ngoh, Si Te; Ji, Lianghui

2015-10-26

Rhodosporidium and Rhodotorula are two genera of oleaginous red yeast with great potential for industrial biotechnology. To date, there is no effective method for inducible expression of proteins and RNAs in these hosts. We have developed a luciferase gene reporter assay based on a new codon-optimized LUC2 reporter gene (RtLUC2), which is flanked with CAR2 homology arms and can be integrated into the CAR2 locus in the nuclear genome at >90 % efficiency. We characterized the upstream DNA sequence of a D-amino acid oxidase gene (DAO1) from R. toruloides ATCC 10657 by nested deletions. By comparing the upstream DNA sequences of several putative DAO1 homologs of Basidiomycetous fungi, we identified a conserved DNA motif with a consensus sequence of AGGXXGXAGX11GAXGAXGG within a 0.2 kb region from the mRNA translation initiation site. Deletion of this motif led to strong mRNA transcription under non-inducing conditions. Interestingly, DAO1 promoter activity was enhanced about fivefold when the 108 bp intron 1 was included in the reporter construct. We identified a conserved CT-rich motif in the intron with a consensus sequence of TYTCCCYCTCCYCCCCACWYCCGA, deletion or point mutations of which drastically reduced promoter strength under both inducing and non-inducing conditions. Additionally, we created a selection marker-free DAO1-null mutant (∆dao1e) which displayed greatly improved inducible gene expression, particularly when both glucose and nitrogen were present in high levels. To avoid adding unwanted peptide to proteins to be expressed, we converted the original translation initiation codon to ATC and re-created a translation initiation codon at the start of exon 2. This promoter, named P DAO1-in1m1 , showed very similar luciferase activity to the wild-type promoter upon induction with D-alanine. The inducible system was tunable by adjusting the levels of inducers, carbon source and nitrogen source. The intron 1-containing DAO1 promoters coupled with a DAO1 null mutant makes an efficient and tight D-amino acid-inducible gene expression system in Rhodosporidium and Rhodotorula genera. The system will be a valuable tool for metabolic engineering and enzyme expression in these yeast hosts.

Stellar encounters involving neutron stars in globular cluster cores

NASA Technical Reports Server (NTRS)

Davies, M. B.; Benz, W.; Hills, J. G.

1992-01-01

Encounters between a 1.4 solar mass neutron star and a 0.8 solar mass red giant (RG) and between a 1.4 solar mass neutron star (NS) and an 0.8 solar mass main-sequence (MS) star have been successfully simulated. In the case of encounters involving an RG, bound systems are produced when the separation at periastron passage R(MIN) is less than about 2.5 R(RG). At least 70 percent of these bound systems are composed of the RG core and NS forming a binary engulfed in a common envelope of what remains of the former RG envelope. Once the envelope is ejected, a tight white dwarf-NS binary remains. For MS stars, encounters with NSs will produce bound systems when R(MIN) is less than about 3.5 R(MS). Some 50 percent of these systems will be single objects with the NS engulfed in a thick disk of gas almost as massive as the original MS star. The ultimate fate of such systems is unclear.

The morphological transformation of red sequence galaxies in clusters since z ˜ 1

NASA Astrophysics Data System (ADS)

Cerulo, P.; Couch, W. J.; Lidman, C.; Demarco, R.; Huertas-Company, M.; Mei, S.; Sánchez-Janssen, R.; Barrientos, L. F.; Muñoz, R.

2017-11-01

The study of galaxy morphology is fundamental to understand the physical processes driving the structural evolution of galaxies. It has long been known that dense environments host high fractions of early-type galaxies and low fractions of late-type galaxies, indicating that the environment affects the structural evolution of galaxies. In this paper, we present an analysis of the morphological composition of red sequence galaxies in a sample of nine galaxy clusters at 0.8 < z < 1.5 drawn from the HAWK-I Cluster Survey (HCS), with the aim of investigating the evolutionary paths of galaxies with different morphologies. We classify galaxies according to their apparent bulge-to-total light ratio and compare with red sequence galaxies from the lower redshift WIde-field Nearby Galaxy-cluster Survey (WINGS) and ESO Distant Cluster Survey (EDisCS). We find that, while the HCS red sequence is dominated by elliptical galaxies at all luminosities and stellar masses, the WINGS red sequence is dominated by elliptical galaxies only at its bright end (MV < -21.0 mag), while S0s become the most frequent class at fainter luminosities. Disc-dominated galaxies comprise 10-14 per cent of the red sequence population in the low (WINGS) and high (HCS) redshift samples, although their fraction increases up to 40 per cent at 0.4 < z < 0.8 (EDisCS). We find a 20 per cent increase in the fraction of S0 galaxies from z ∼ 1.5 to 0.05 on the red sequence. These results suggest that elliptical and S0 galaxies follow different evolutionary histories and, in particular, that S0 galaxies result, at least at intermediate luminosities (-22.0 < MV < -20.0), from the morphological transformation of quiescent spiral galaxies.

Satellite DNA Sequences in Canidae and Their Chromosome Distribution in Dog and Red Fox.

PubMed

Vozdova, Miluse; Kubickova, Svatava; Cernohorska, Halina; Fröhlich, Jan; Rubes, Jiri

2016-01-01

Satellite DNA is a characteristic component of mammalian centromeric heterochromatin, and a comparative analysis of its evolutionary dynamics can be used for phylogenetic studies. We analysed satellite and satellite-like DNA sequences available in NCBI for 4 species of the family Canidae (red fox, Vulpes vulpes, VVU; domestic dog, Canis familiaris, CFA; arctic fox, Vulpes lagopus, VLA; raccoon dog, Nyctereutes procyonoides procyonoides, NPR) by comparative sequence analysis, which revealed 86-90% intraspecies and 76-79% interspecies similarity. Comparative fluorescence in situ hybridisation in the red fox and dog showed signals of the red fox satellite probe in canine and vulpine autosomal centromeres, on VVUY, B chromosomes, and in the distal parts of VVU9q and VVU10p which were shown to contain nucleolus organiser regions. The CFA satellite probe stained autosomal centromeres only in the dog. The CFA satellite-like DNA did not show any significant sequence similarity with the satellite DNA of any species analysed and was localised to the centromeres of 9 canine chromosome pairs. No significant heterochromatin block was detected on the B chromosomes of the red fox. Our results show extensive heterogeneity of satellite sequences among Canidae and prove close evolutionary relationships between the red and arctic fox. © 2017 S. Karger AG, Basel.

Positioning the red deer (Cervus elaphus) hunted by the Tyrolean Iceman into a mitochondrial DNA phylogeny.

PubMed

Olivieri, Cristina; Marota, Isolina; Rizzi, Ermanno; Ermini, Luca; Fusco, Letizia; Pietrelli, Alessandro; De Bellis, Gianluca; Rollo, Franco; Luciani, Stefania

2014-01-01

In the last years several phylogeographic studies of both extant and extinct red deer populations have been conducted. Three distinct mitochondrial lineages (western, eastern and North-African/Sardinian) have been identified reflecting different glacial refugia and postglacial recolonisation processes. However, little is known about the genetics of the Alpine populations and no mitochondrial DNA sequences from Alpine archaeological specimens are available. Here we provide the first mitochondrial sequences of an Alpine Copper Age Cervus elaphus. DNA was extracted from hair shafts which were part of the remains of the clothes of the glacier mummy known as the Tyrolean Iceman or Ötzi (5,350-5,100 years before present). A 2,297 base pairs long fragment was sequenced using a mixed sequencing procedure based on PCR amplifications and 454 sequencing of pooled amplification products. We analyzed the phylogenetic relationships of the Alpine Copper Age red deer's haplotype with haplotypes of modern and ancient European red deer. The phylogenetic analyses showed that the haplotype of the Alpine Copper Age red deer falls within the western European mitochondrial lineage in contrast with the current populations from the Italian Alps belonging to the eastern lineage. We also discussed the phylogenetic relationships of the Alpine Copper Age red deer with the populations from Mesola Wood (northern Italy) and Sardinia.

The Provincial Reconstruction Teams in Afghanistan - A Model for Future Nation Building Operations

DTIC Science & Technology

2009-05-01

public at home. In the case of Germany, restrictions and tight rules of engagements (RoE) are the political solution. Using PRTs can make the...concept w ith integrated strategies on nation-builder’s is hinde red by departmental egoism , intergovernmental rivalries, and political shortsightedness

Sequence divergence of the red and green visual pigments in great apes and humans.

PubMed Central

Deeb, S S; Jorgensen, A L; Battisti, L; Iwasaki, L; Motulsky, A G

1994-01-01

We have determined the coding sequences of red and green visual pigment genes of the chimpanzee, gorilla, and orangutan. The deduced amino acid sequences of these pigments are highly homologous to the equivalent human pigments. None of the amino acid differences occurred at sites that were previously shown to influence pigment absorption characteristics. Therefore, we predict the spectra of red and green pigments of the apes to have wavelengths of maximum absorption that differ by < 2 nm from the equivalent human pigments and that color vision in these nonhuman primates will be very similar, if not identical, to that in humans. A total of 14 within-species polymorphisms (6 involving silent substitutions) were observed in the coding sequences of the red and green pigment genes of the great apes. Remarkably, the polymorphisms at 6 of these sites had been observed in human populations, suggesting that they predated the evolution of higher primates. Alleles at polymorphic sites were often shared between the red and green pigment genes. The average synonymous rate of divergence of red from green sequences was approximately 1/10th that estimated for other proteins of higher primates, indicating the involvement of gene conversion in generating these polymorphisms. The high degree of homology and juxtaposition of these two genes on the X chromosome has promoted unequal recombination and/or gene conversion that led to sequence homogenization. However, natural selection operated to maintain the degree of separation in peak absorbance between the red and green pigments that resulted in optimal chromatic discrimination. This represents a unique case of molecular coevolution between two homologous genes that functionally interact at the behavioral level. PMID:8041777

Laser Plasma Soft X-ray Microscope with Wolter Mirrors for Observation of Biological Specimens in Air

NASA Astrophysics Data System (ADS)

Hoshino, Masato; Aoki, Sadao

2006-02-01

A laser plasma soft X-ray microscope with Wolter mirrors was developed so that specimens could be set in the atmosphere. Silicon nitride membranes 100 nm thick were used as vacuum-tight windows. Using relatively large windows (0.46× 0.46 mm2), an adequate working distance for samples, which was approximately 1.2 mm, was assured. The endurance of the vacuum-tight window was measured briefly. Dry biological cells could be observed with resolution better than 100 nm. A preliminary observation of wet biological cells was carried out using a wet environmental sample holder which was composed of only two sheets of silicon nitride membrane. An X-ray micrograph of wet red blood cells from a chicken was obtained without apparent effects of radiation damage. The properties of a vacuum-tight window and a wet sample holder are discussed.

Native red electrophoresis--a new method suitable for separation of native proteins.

PubMed

Dráb, Tomáš; Kračmerová, Jana; Tichá, Ivana; Hanzlíková, Eva; Tichá, Marie; Ryšlavá, Helena; Doubnerová, Veronika; Maňásková-Postlerová, Pavla; Liberda, Jiří

2011-12-01

A new type of native electrophoresis was developed to separate and characterize proteins. In this modification of the native blue electrophoresis, the dye Ponceau Red S is used instead of Coomassie Brilliant Blue to impose uniform negative charge on proteins to enable their electrophoretic separation according to their relative molecular masses. As Ponceau Red S binds less tightly to proteins, in comparison with Coomassie Blue, it can be easily removed after the electrophoretic separation and a further investigation of protein properties is made possible (e.g. an enzyme detection or electroblotting). The tested proteins also kept their native properties (enzyme activity or aggregation state). Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Positioning the Red Deer (Cervus elaphus) Hunted by the Tyrolean Iceman into a Mitochondrial DNA Phylogeny

PubMed Central

Olivieri, Cristina; Marota, Isolina; Rizzi, Ermanno; Ermini, Luca; Fusco, Letizia; Pietrelli, Alessandro; De Bellis, Gianluca; Rollo, Franco; Luciani, Stefania

2014-01-01

In the last years several phylogeographic studies of both extant and extinct red deer populations have been conducted. Three distinct mitochondrial lineages (western, eastern and North-African/Sardinian) have been identified reflecting different glacial refugia and postglacial recolonisation processes. However, little is known about the genetics of the Alpine populations and no mitochondrial DNA sequences from Alpine archaeological specimens are available. Here we provide the first mitochondrial sequences of an Alpine Copper Age Cervus elaphus. DNA was extracted from hair shafts which were part of the remains of the clothes of the glacier mummy known as the Tyrolean Iceman or Ötzi (5,350–5,100 years before present). A 2,297 base pairs long fragment was sequenced using a mixed sequencing procedure based on PCR amplifications and 454 sequencing of pooled amplification products. We analyzed the phylogenetic relationships of the Alpine Copper Age red deer's haplotype with haplotypes of modern and ancient European red deer. The phylogenetic analyses showed that the haplotype of the Alpine Copper Age red deer falls within the western European mitochondrial lineage in contrast with the current populations from the Italian Alps belonging to the eastern lineage. We also discussed the phylogenetic relationships of the Alpine Copper Age red deer with the populations from Mesola Wood (northern Italy) and Sardinia. PMID:24988290

The tight junction protein ZO-1 and an interacting transcription factor regulate ErbB-2 expression

PubMed Central

Balda, Maria S.; Matter, Karl

2000-01-01

Epithelial tight junctions regulate paracellular diffusion and restrict the intermixing of apical and basolateral plasma membrane components. We now identify a Y-box transcription factor, ZONAB (ZO-1-associated nucleic acid-binding protein), that binds to the SH3 domain of ZO-1, a submembrane protein of tight junctions. ZONAB localizes to the nucleus and at tight junctions, and binds to sequences of specific promoters containing an inverted CCAAT box. In reporter assays, ZONAB and ZO-1 functionally interact in the regulation of the ErbB-2 promoter in a cell density-dependent manner. In stably transfected overexpressing cells, ZO-1 and ZONAB control expression of endogenous ErbB-2 and function in the regulation of paracellular permeability. These data indicate that tight junctions directly participate in the control of gene expression and suggest that they function in the regulation of epithelial cell differentiation. PMID:10790369

A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar

USDA-ARS?s Scientific Manuscript database

A small fast neutron mutant population has been established from Phaseolus vulgaris cv. Red Hawk. We leveraged the available P. vulgaris genome sequence and high throughput next generation DNA sequencing to examine the genomic structure of five Phaseolus vulgaris cv. Red Hawk fast neutron mutants wi...

Plasmon excitations in doped square-lattice atomic clusters

NASA Astrophysics Data System (ADS)

Wang, Yaxin; Yu, Ya-Bin

2017-12-01

Employing the tight-binding model, we theoretically study the properties of the plasmon excitations in doped square-lattice atomic clusters. The results show that the dopant atoms would blur the absorption spectra, and give rise to extra plasmon resonant peaks as reported in the literature; however, our calculated external-field induced oscillating charge density shows that no obvious evidences indicate the so-called local mode of plasmon appearing in two-dimensional-doped atomic clusters, but the dopants may change the symmetry of the charge distribution. Furthermore, we show that the disorder of the energy level due to dopant makes the absorption spectrum has a red- or blue-shift, which depends on the position of impurities; disorder of hopping due to dopant makes a blue- or red-shift, a larger (smaller) hopping gives a blue-shift (red-shift); and a larger (smaller) host-dopant and dopant-dopant intersite coulomb repulsion induces a blue-shift (red-shift).

Neighboring genes shaping a single adaptive mimetic trait.

PubMed

Pardo-Diaz, Carolina; Jiggins, Chris D

2014-01-01

The colorful wing patterns of Heliconius butterflies represent an excellent system in which to study the genetic and developmental control of adaptation and convergence. Using qRT-PCR and in situ hybridization on developing wings of the co-mimic species Heliconius melpomene and Heliconius erato, we have profiled the expression of three candidate genes located in the genomic locus controlling red color pattern variation. We found convergent domains of gene expression in H. melpomene and H. erato associated with red wing elements in the two genes optix and kinesin. During early pupal development of both species, the expression of optix perfectly associated with all red pattern elements whereas that of kinesin was specifically correlated with the presence of the red forewing band. These results provide evidence for the use of these two tightly linked patterning genes, acting together to create convergent wing phenotypes in Heliconius and constituting a hotspot of adaptation. © 2013 Wiley Periodicals, Inc.

Insertion sequences enrichment in extreme Red sea brine pool vent.

PubMed

Elbehery, Ali H A; Aziz, Ramy K; Siam, Rania

2017-03-01

Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world's largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.

Accurate identification of RNA editing sites from primitive sequence with deep neural networks.

PubMed

Ouyang, Zhangyi; Liu, Feng; Zhao, Chenghui; Ren, Chao; An, Gaole; Mei, Chuan; Bo, Xiaochen; Shu, Wenjie

2018-04-16

RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filtering steps, resulting in a cumbersome, time-consuming identification process. Moreover, these methods have limited generalizability and applicability in species with insufficient genomic annotations or in conditions of limited prior knowledge. We developed DeepRed, a deep learning-based method that identifies RNA editing from primitive RNA sequences without prior-knowledge-based filtering steps or genomic annotations. DeepRed achieved 98.1% and 97.9% area under the curve (AUC) in training and test sets, respectively. We further validated DeepRed using experimentally verified U87 cell RNA-seq data, achieving 97.9% positive predictive value (PPV). We demonstrated that DeepRed offers better prediction accuracy and computational efficiency than current methods with large-scale, mass RNA-seq data. We used DeepRed to assess the impact of multiple factors on editing identification with RNA-seq data from the Association of Biomolecular Resource Facilities and Sequencing Quality Control projects. We explored developmental RNA editing pattern changes during human early embryogenesis and evolutionary patterns in Drosophila species and the primate lineage using DeepRed. Our work illustrates DeepRed's state-of-the-art performance; it may decipher the hidden principles behind RNA editing, making editing detection convenient and effective.

Structural and Biophysical Characterization of the Mycobacterium tuberculosis Protein Rv0577, a Protein Associated with Neutral Red Staining of Virulent Tuberculosis Strains and Homologue of the Streptomyces coelicolor Protein KbpA

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

Buchko, Garry W.; Echols, Nathaniel; Flynn, E. Megan

The 261-residue Mycobacterium tuberculosis protein Rv0577 is a prominent antigen in tuberculosis patients, the responsible component for neutral red staining of virulent strains of M. tuberculosis, a putative component in a methylglyoxal detoxification pathway, and an agonist of toll-like receptor 2. It also has 36% sequence identity to AfsK-binding protein A (KbpA), a component in the complex secondary metabolite pathways in the Streptomycetes genus from which many commercial antibiotics are derived. To gain insight into the biological function of Rv0577 and the family of KpbA kinase regulators, the crystal structure for Rv0577 was determined to a resolution of 1.75 Åmore » (3OXH), binding properties with neutral red and deoxyadenosine (Ado) surveyed, backbone dynamics measured, and thermal stability assayed by CD spectroscopy. The protein is composed of four approximate repeats with an topology arranged radially in consecutive pairs to form two continuous eight-strand -sheets capped on both ends with an -helix. The two -sheets intersect in the center at roughly a right angle and form an asymmetric deep “saddle” on both sides of the protein, saddle one (P11 to A129) and saddle two (L143 to A258), that may serve to bind ligands. NMR chemical shift perturbation experiments show that neutral red binds to Rv0577, further cementing the role of Rv0577 in the neutral red staining of virulent strains of M. tuberculosis. Similar experiments show that adenosine also bind to Rv0577, although less tightly, with estimated dissociation constants of 4.1 ± 0.3 mM for saddle one and > 1 M for saddle two. Heteronuclear steady-state {1H}-15N NOE, T1, and T2 values were generally uniform through-out the sequence with only a few modest pockets of differences suggestive of slightly different motion in loops between -strands in saddle 1. Circular dichroism spectroscopy characterization of the thermal stability of Rv0577 indicated irreversible unfolding upon heating with an estimated melting temperature of 56 °C. While it is not known if Rv0577 has a kinase regulatory role similar to its Streptomyces homolog KbpA, protein kinase and phosphatase signaling help M. tuberculosis adapt to the hostile host environment during infections. Consequently, new anti-tuberculosis drugs targeting Rv0577 may act by interfering with multiple mechanisms; a potential signaling machinery as well as toll-like receptor 2 activation and the methylglyoxal detoxification pathway.« less

21 CFR 358.650 - Labeling of pediculicide drug products.

Code of Federal Regulations, 2010 CFR

2010-04-01

...) of this chapter. (2) “Do not use [bullet] 1 near eyes [bullet] inside nose, mouth, or vagina [bullet... [bullet] keep eyes tightly closed and protect eyes with a washcloth or towel [bullet] if product gets in eyes, flush with water right away [bullet] scalp itching or redness may occur”. (5) “Stop use and ask a...

Spectroscopic characterization of galaxy clusters in RCS-1: spectroscopic confirmation, redshift accuracy, and dynamical mass-richness relation

NASA Astrophysics Data System (ADS)

Gilbank, David G.; Barrientos, L. Felipe; Ellingson, Erica; Blindert, Kris; Yee, H. K. C.; Anguita, T.; Gladders, M. D.; Hall, P. B.; Hertling, G.; Infante, L.; Yan, R.; Carrasco, M.; Garcia-Vergara, Cristina; Dawson, K. S.; Lidman, C.; Morokuma, T.

2018-05-01

We present follow-up spectroscopic observations of galaxy clusters from the first Red-sequence Cluster Survey (RCS-1). This work focuses on two samples, a lower redshift sample of ˜30 clusters ranging in redshift from z ˜ 0.2-0.6 observed with multiobject spectroscopy (MOS) on 4-6.5-m class telescopes and a z ˜ 1 sample of ˜10 clusters 8-m class telescope observations. We examine the detection efficiency and redshift accuracy of the now widely used red-sequence technique for selecting clusters via overdensities of red-sequence galaxies. Using both these data and extended samples including previously published RCS-1 spectroscopy and spectroscopic redshifts from SDSS, we find that the red-sequence redshift using simple two-filter cluster photometric redshifts is accurate to σz ≈ 0.035(1 + z) in RCS-1. This accuracy can potentially be improved with better survey photometric calibration. For the lower redshift sample, ˜5 per cent of clusters show some (minor) contamination from secondary systems with the same red-sequence intruding into the measurement aperture of the original cluster. At z ˜ 1, the rate rises to ˜20 per cent. Approximately ten per cent of projections are expected to be serious, where the two components contribute significant numbers of their red-sequence galaxies to another cluster. Finally, we present a preliminary study of the mass-richness calibration using velocity dispersions to probe the dynamical masses of the clusters. We find a relation broadly consistent with that seen in the local universe from the WINGS sample at z ˜ 0.05.

A Multiplex PCR assay to differentiate between dog and red fox.

PubMed

Weissenberger, M; Reichert, W; Mattern, R

2011-11-01

Foxes are frequently the cause of car accidents in Baden-Württemberg (BW, Germany). The domestic dog (Canis familiaris) is in close relation to the red fox (Vulpes vulpes) and the silver fox which is a coat colour variant of the red fox. As insurance claims that involve accidents with animals require authentication, we analyzed frequency distribution and allele sizes in two canine microsatellite loci in 26 dogs (different breeds) and 19 red foxes of the region of BW, Germany. Moreover, sequencing analysis was performed. Red foxes exhibited only 1 allele at each microsatellite locus, whereas in dog 7 alleles at the CPH4 locus and 6 alleles at the CPH12 locus were detected. Sequences of PCR products from the two species revealed several differences between dogs and foxes. We established a sequenced allelic ladder and give population data from dogs and red foxes from the region of BW, Germany. Using microsatellite polymorphisms is efficient in differentiating between dogs and foxes in forensic casework. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

EVIDENCE FOR THE UNIVERSALITY OF PROPERTIES OF RED-SEQUENCE GALAXIES IN X-RAY- AND RED-SEQUENCE-SELECTED CLUSTERS AT z ∼ 1

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

Foltz, R.; Wilson, G.; DeGroot, A.

We study the slope, intercept, and scatter of the color–magnitude and color–mass relations for a sample of 10 infrared red-sequence-selected clusters at z ∼ 1. The quiescent galaxies in these clusters formed the bulk of their stars above z ≳ 3 with an age spread Δt ≳ 1 Gyr. We compare UVJ color–color and spectroscopic-based galaxy selection techniques, and find a 15% difference in the galaxy populations classified as quiescent by these methods. We compare the color–magnitude relations from our red-sequence selected sample with X-ray- and photometric-redshift-selected cluster samples of similar mass and redshift. Within uncertainties, we are unable tomore » detect any difference in the ages and star formation histories of quiescent cluster members in clusters selected by different methods, suggesting that the dominant quenching mechanism is insensitive to cluster baryon partitioning at z ∼ 1.« less

Reaction Analysis of Shocked Nitromethane using Extended Lagrangian Born-Oppenheimer Molecular Dynamics

NASA Astrophysics Data System (ADS)

Perriot, Romain; Kober, Ed; Mniszewski, Sue; Martinez, Enrique; Niklasson, Anders; Yang, Ping; McGrane, Shawn; Cawkwell, Marc

2017-06-01

Characterizing the complex, rapid reactions of energetic materials under conditions of high temperatures and pressures presents strong experimental and computational challenges. The recently developed extended Lagrangian Born-Oppenheimer molecular dynamics formalism enables the long-term conservation of the total energy in microcanonical trajectories, and using a density functional tight binding formulation provides good chemical accuracy. We use this combined approach to study the evolution of temperature, pressure, and chemical species in shock-compressed liquid nitromethane over hundreds of picoseconds. The chemical species seen in nitromethane under shock compression are compared with those seen under static high temperature conditions. A reduced-order representation of the complex sequence of chemical reactions that characterize this system has been developed from the molecular dynamics simulations by focusing on classes of chemical reactions rather than specific molecular species. Time-resolved infra-red vibrational spectra were also computed from the molecular trajectories and compared to the chemical analysis. These spectra provide a time history of the species present in the system that can be compared directly with recent experiments at LANL.

An outburst powered by the merging of two stars inside the envelope of a giant

NASA Astrophysics Data System (ADS)

Hillel, Shlomi; Schreier, Ron; Soker, Noam

2017-11-01

We conduct 3D hydrodynamical simulations of energy deposition into the envelope of a red giant star as a result of the merger of two close main sequence stars or brown dwarfs, and show that the outcome is a highly non-spherical outflow. Such a violent interaction of a triple stellar system can explain the formation of `messy', I.e. lacking any kind of symmetry, planetary nebulae and similar nebulae around evolved stars. We do not simulate the merging process, but simply assume that after the tight binary system enters the envelope of the giant star the interaction with the envelope causes the two components, stars or brown dwarfs, to merge and liberate gravitational energy. We deposit the energy over a time period of about 9 h, which is about 1 per cent of the the orbital period of the merger product around the centre of the giant star. The ejection of the fast hot gas and its collision with previously ejected mass are very likely to lead to a transient event, I.e. an intermediate luminosity optical transient.

The complete mitochondrial genome sequence of the Tibetan red fox (Vulpes vulpes montana).

PubMed

Zhang, Jin; Zhang, Honghai; Zhao, Chao; Chen, Lei; Sha, Weilai; Liu, Guangshuai

2015-01-01

In this study, the complete mitochondrial genome of the Tibetan red fox (Vulpes Vulpes montana) was sequenced for the first time using blood samples obtained from a wild female red fox captured from Lhasa in Tibet, China. Qinghai--Tibet Plateau is the highest plateau in the world with an average elevation above 3500 m. Sequence analysis showed it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region (CR). The variable tandem repeats in CR is the main reason of the length variability of mitochondrial genome among canide animals.

Pore-throat sizes in sandstones, siltstones, and shales: Reply

USGS Publications Warehouse

Nelson, Philip H.

2011-01-01

In his discussion of my article (Nelson, 2009), W. K. Camp takes issue with the concept that buoyancy is not the dominant force in forming and maintaining the distribution of gas in tight-gas accumulations (Camp, 2011). I will restrict my response to the issues he raised regarding buoyant versus nonbuoyant drive and to a few comments regarding water saturation and production. I claim that the pressure generated in petroleum source rocks (Pg), instead of the buoyancy pressure (Pb), provides the energy to charge most tight sandstones with gas. The arguments are fourfold: (1) buoyant columns of sufficient height seldom exist in low-permeability sand-shale sequences, (2) tight-gas systems display a pressure profile that declines instead of increases upward, (3) gas is pervasive in overpressured systems, and (4) source rocks can generate pore pressures sufficiently high to charge tight sandstones.

Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese

PubMed Central

Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle

2015-01-01

Clostridium tyrobutyricum is the main microorganism responsible for late blowing defect in cheeses. Here, we present the draft genome sequences of two C. tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative coding sequences, respectively. PMID:25767226

THE RED SEQUENCE AT BIRTH IN THE GALAXY CLUSTER Cl J1449+0856 AT z = 2

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

Strazzullo, V.; Pannella, M.; Daddi, E.

We use Hubble Space Telescope /WFC3 imaging to study the red population in the IR-selected, X-ray detected, low-mass cluster Cl J1449+0856 at z = 2, one of the few bona fide established clusters discovered at this redshift, and likely a typical progenitor of an average massive cluster today. This study explores the presence and significance of an early red sequence in the core of this structure, investigating the nature of red-sequence galaxies, highlighting environmental effects on cluster galaxy populations at high redshift, and at the same time underlining similarities and differences with other distant dense environments. Our results suggest thatmore » the red population in the core of Cl J1449+0856 is made of a mixture of quiescent and dusty star-forming galaxies, with a seedling of the future red sequence already growing in the very central cluster region, and already characterizing the inner cluster core with respect to lower-density environments. On the other hand, the color–magnitude diagram of this cluster is definitely different from that of lower-redshift z ≲ 1 clusters, as well as of some rare particularly evolved massive clusters at similar redshift, and it is suggestive of a transition phase between active star formation and passive evolution occurring in the protocluster and established lower-redshift cluster regimes.« less

A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes).

PubMed

Kutschera, Verena E; Lecomte, Nicolas; Janke, Axel; Selva, Nuria; Sokolov, Alexander A; Haun, Timm; Steyer, Katharina; Nowak, Carsten; Hailer, Frank

2013-06-05

Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan's northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories.

A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes)

PubMed Central

2013-01-01

Background Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. Results Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. Conclusions The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan’s northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories. PMID:23738594

High-cell-density cultivation of recombinant Escherichia coli, purification and characterization of a self-sufficient biosynthetic octane ω-hydroxylase.

PubMed

Bordeaux, Mélanie; de Girval, Diane; Rullaud, Robin; Subileau, Maeva; Dubreucq, Eric; Drone, Jullien

2014-01-01

We have recently described the biocatalytic characterization of a self-sufficent biosynthetic alkane hydroxylase based on CYP153A13a from Alcanivorax borkumensis SK2 (thereafter A13-Red). Despite remarkable regio- and chemo-selectivity, A13-Red suffers of a difficult-to-reproduce expression and moderate operational stability. In this study, we focused our efforts on the production of A13-Red using high-cell-density cultivation (HCDC) of recombinant Escherichia coli. We achieved 455 mg (5,000 nmol) of functional enzyme per liter of culture. Tight control of cultivation parameters rendered the whole process highly reproducible compared with flask cultivations. We optimized the purification of the biocatalyst that can be performed in either two or three steps depending on the application needed to afford A13-Red up to 95 % homogeneous. We investigated different reaction conditions and found that the total turnover numbers of A13-Red during the in vitro hydroxylation of n-octane could reach up to 3,250 to produce 1-octanol (1.6 mM) over a period of 78 h.

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

Park, Hong Soo; Lee, Myung Gyoon, E-mail: hspark@astro.snu.ac.kr, E-mail: mglee@astro.snu.ac.kr

We present a determination of the two-dimensional shape parameters of the blue and red globular cluster systems (GCSs) in a large number of elliptical galaxies and lenticular galaxies (early-type galaxies, called ETGs). We use a homogeneous data set of the globular clusters in 23 ETGs obtained from the HST/ACS Virgo Cluster Survey. The position angles of both blue and red GCSs show a correlation with those of the stellar light distribution, showing that the major axes of the GCSs are well aligned with those of their host galaxies. However, the shapes of the red GCSs show a tight correlation withmore » the stellar light distribution as well as with the rotation property of their host galaxies, while the shapes of the blue GCSs do much less. These provide clear geometric evidence that the origins of the blue and red globular clusters are distinct and that ETGs may have dual halos: a blue (metal-poor) halo and a red (metal-rich) halo. These two halos show significant differences in metallicity, structure, and kinematics, indicating that they are formed in two distinguishable ways. The red halos might have formed via dissipational processes with rotation, while the blue halos are through accretion.« less

Growth and photomorphogenesis of pepper plants under red light-emitting diodes with supplemental blue or far-red lighting

NASA Technical Reports Server (NTRS)

Brown, C. S.; Schuerger, A. C.; Sager, J. C.

1995-01-01

Light-emitting diodes (LEDs) are a potential irradiation source for intensive plant culture systems and photobiological research. They have small size, low mass, a long functional life, and narrow spectral output. In this study, we measured the growth and dry matter partitioning of 'Hungarian Wax' pepper (Capsicum annuum L.) plants grown under red LEDs compared with similar plants grown under red LEDs with supplemental blue or far-red radiation or under broad spectrum metal halide (MH) lamps. Additionally, we describe the thermal and spectral characteristics of these sources. The LEDs used in this study had a narrow bandwidth at half peak height (25 nm) and a focused maximum spectral output at 660 nm for the red and 735 nm for the far-red. Near infrared radiation (800 to 3000 nm) was below detection and thermal infrared radiation (3000 to 50,000 nm) was lower in the LEDs compared to the MH source. Although the red to far-red ratio varied considerably, the calculated phytochrome photostationary state (phi) was only slightly different between the radiation sources. Plant biomass was reduced when peppers were grown under red LEDs in the absence of blue wavelengths compared to plants grown under supplemental blue fluorescent lamps or MH lamps. The addition of far-red radiation resulted in taller plants with greater stem mass than red LEDs alone. There were fewer leaves under red or red plus far-red radiation than with lamps producing blue wavelengths. These results indicate that red LEDs may be suitable, in proper combination with other wavelengths of light, for the culture of plants in tightly controlled environments such as space-based plant culture systems.

Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese.

PubMed

Storari, Michelangelo; Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle

2015-03-12

Clostridium tyrobutyricum is the main microorganism responsible for late blowing defect in cheeses. Here, we present the draft genome sequences of two C. tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative coding sequences, respectively. Copyright © 2015 Storari et al.

Genome sequence of "Candidatus Mycoplasma haemolamae" strain purdue, a red blood cell pathogen of alpacas (Vicugna pacos) and llamas (Lama glama).

PubMed

Guimaraes, Ana M S; Toth, Balazs; Santos, Andrea P; do Nascimento, Naíla C; Kritchevsky, Janice E; Messick, Joanne B

2012-11-01

We report the complete genome sequence of "Candidatus Mycoplasma haemolamae," an endemic red-cell pathogen of camelids. The single, circular chromosome has 756,845 bp, a 39.3% G+C content, and 925 coding sequences (CDSs). A great proportion (49.1%) of these CDSs are organized into paralogous gene families, which can now be further explored with regard to antigenic variation.

From Red Cells to Soft Porous Lubrication

NASA Astrophysics Data System (ADS)

Wu, Qianhong; Gacka, Thomas; Nathan, Rungun; Crawford, Robert; Vucbmss Team

2014-11-01

Biological scientists have wondered, since the motion of red cells was first observed in capillaries, how the highly flexible red cell can move with so little friction in tightly fitting microvessels without being damaged or undergoing hemolysis. Theoretical studies (Feng and Weinbaum, 2000, JFM; Wu et al., 2004, PRL) attributed this frictionless motion to the dramatically enhanced hydrodynamic lifting force generated inside the soft, porous, endothelial surface layer (ESL) covering the inner surfaces of our capillaries, as a red blood cell glides over it. Herein we report the first experimental examination of this concept. The results conclusively demonstrate that significant fraction of the overall lifting force generated in a soft porous layer as a planing surface glides over it, is contributed by the pore fluid pressure, and thus frictional loss is reduced significantly. Moreover, the experimental predictions showed excellent agreement with the experimental data. This finding has the potential of dramatically changing existing lubrication approaches, and can result in substantial savings in energy consumption and thus reduction in greenhouse gas emissions.

Identification of sequence-related amplified polymorphism markers linked to the red leaf trait in ornamental kale (Brassica oleracea L. var. acephala).

PubMed

Wang, Y S; Liu, Z Y; Li, Y F; Zhang, Y; Yang, X F; Feng, H

2013-04-02

Artistic diversiform leaf color is an important agronomic trait that affects the market value of ornamental kale. In the present study, genetic analysis showed that a single-dominant gene, Re (red leaf), determines the red leaf trait in ornamental kale. An F2 population consisting of 500 individuals from the cross of a red leaf double-haploid line 'D05' with a white leaf double-haploid line 'D10' was analyzed for the red leaf trait. By combining bulked segregant analysis and sequence-related amplified polymorphism technology, we identified 3 markers linked to the Re/re locus. A genetic map of the Re locus was constructed using these sequence-related amplified polymorphism markers. Two of the markers, Me8Em4 and Me8Em17, were located on one side of Re/re at distances of 2.2 and 6.4 cM, whereas the other marker, Me9Em11, was located on the other side of Re/re at a distance of 3.7 cM. These markers could be helpful for the subsequent cloning of the red trait gene and marker-assisted selection in ornamental kale breeding programs.

Biomarker Discovery and Mechanistic Studies of Prostate Cancer using Targeted Proteomic Approaches

DTIC Science & Technology

2012-07-01

basigin in Drosophila ) tightly regulates cytoskeleton rearrangement in Drosophila melanogaster [23]. Based on the present results and the existing...from OligoEngine according to the manufac- turer’s instruction. Plasmids were amplified in DH5a cell and confirmed by sequencing . Subconfluent cell...electrophoresis and the results are shown in Figure 1 (Panel C). The RT-PCR products were cloned and subjected to DNA sequenc - ing. The sequencing

The Optical Gravitational Lensing Experiment. Ellipsoidal Variability of Red Giants in the Large Magellanic Cloud

NASA Astrophysics Data System (ADS)

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

2004-12-01

We used the OGLE-II and OGLE-III photometry of red giants in the Large Magellanic Cloud to select and study objects revealing ellipsoidal variability. We detected 1546 candidates for long period ellipsoidal variables and 121 eclipsing binary systems with clear ellipsoidal modulation. The ellipsoidal red giants follow a period--luminosity (PL) relationship (sequence E), and the scatter of the relation is correlated with the amplitude of variability: the larger the amplitude, the smaller the scatter. We note that some of the ellipsoidal candidates exhibit simultaneously OGLE Small Amplitude Red Giants pulsations. Thus, in some cases the Long Secondary Period (LSP) phenomenon can be explained by the ellipsoidal modulation. We also select about 1600 red giants with distinct LSP, which are not ellipsoidal variables. We discover that besides the sequence D in the PL diagram known before, the LSP giants form additional less numerous sequence for longer periods. We notice that the PL sequence of the ellipsoidal candidates is a direct continuation of the LSP sequence toward fainter stars, what might suggest that the LSP phenomenon is related to binarity but there are strong arguments against such a possibility. About 10% of the presented light curves reveal clear deformation by the eccentricity of the system orbits. The largest estimated eccentricity in our sample is about 0.4. All presented data, including individual BVI observations and finding charts are available from the OGLE Internet archive.

Genome Sequence of “Candidatus Mycoplasma haemolamae” Strain Purdue, a Red Blood Cell Pathogen of Alpacas (Vicugna pacos) and Llamas (Lama glama)

PubMed Central

Toth, Balazs; Santos, Andrea P.; do Nascimento, Naíla C.; Kritchevsky, Janice E.

2012-01-01

We report the complete genome sequence of “Candidatus Mycoplasma haemolamae,” an endemic red-cell pathogen of camelids. The single, circular chromosome has 756,845 bp, a 39.3% G+C content, and 925 coding sequences (CDSs). A great proportion (49.1%) of these CDSs are organized into paralogous gene families, which can now be further explored with regard to antigenic variation. PMID:23105057

The rDNA ITS region in the lessepsian marine angiosperm Halophila stipulacea (Forssk.) Aschers. (Hydrocharitaceae): intragenomic variability and putative pseudogenic sequences.

PubMed

Ruggiero, Maria Valeria; Procaccini, Gabriele

2004-01-01

Halophila stipulacea is a dioecious marine angiosperm, widely distributed along the western coasts of the Indian Ocean and the Red Sea. This species is thought to be a Lessepsian immigrant that entered the Mediterranean Sea from the Red Sea after the opening of the Suez Canal (1869). Previous studies have revealed both high phenotypic and genetic variability in Halophila stipulacea populations from the western Mediterranean basin. In order to test the hypothesis of a Lessepsian introduction, we compare genetic polymorphism between putative native (Red Sea) and introduced (Mediterranean) populations through rDNA ITS region (ITS1-5.8S-ITS2) sequence analysis. A high degree of intraindividual variability of ITS sequences was found. Most of the intragenomic polymorphism was due to pseudogenic sequences, present in almost all individuals. Features of ITS functional sequences and pseudogenes are described. Possible causes for the lack of homogenization of ITS paralogues within individuals are discussed.

Ages of intermediate-age Magellanic Cloud star clusters

NASA Technical Reports Server (NTRS)

Flower, P. J.

1984-01-01

Ages of intermediate-age Large Magellanic Cloud star clusters have been estimated without locating the faint, unevolved portion of cluster main sequences. Six clusters with established color-magnitude diagrams were selected for study: SL 868, NGC 1783, NGC 1868, NGC 2121, NGC 2209, and NGC 2231. Since red giant photometry is more accurate than the necessarily fainter main-sequence photometry, the distributions of red giants on the cluster color-magnitude diagrams were compared to a grid of 33 stellar evolutionary tracks, evolved from the main sequence through core-helium exhaustion, spanning the expected mass and metallicity range for Magellanic Cloud cluster red giants. The time-dependent behavior of the luminosity of the model red giants was used to estimate cluster ages from the observed cluster red giant luminosities. Except for the possibility of SL 868 being an old globular cluster, all clusters studied were found to have ages less than 10 to the 9th yr. It is concluded that there is currently no substantial evidence for a major cluster population of large, populous clusters greater than 10 to the 9th yr old in the Large Magellanic Cloud.

Association of MC3R gene polymorphisms with body weight in the red fox and comparative gene organization in four canids.

PubMed

Skorczyk, A; Flisikowski, K; Szydlowski, M; Cieslak, J; Fries, R; Switonski, M

2011-02-01

There are five genes encoding melanocortin receptors. Among canids, the genes have mainly been studied in the dog (MC1R, MC2R and MC4R). The MC4R gene has also been analysed in the red fox. In this report, we present a study of chromosome localization, comparative sequence analysis and polymorphism of the MC3R gene in the dog, red fox, arctic fox and Chinese raccoon dog. The gene was localized by FISH to the following chromosome: 24q24-25 in the dog, 14p16 in the red fox, 18q13 in the arctic fox and NPP4p15 in the Chinese raccoon dog. A high identity level of the MC3R gene sequences was observed among the species, ranging from 96.0% (red fox--Chinese raccoon dog) to 99.5% (red fox--arctic fox). Altogether, eight polymorphic sites were found in the red fox, six in the Chinese raccoon dog and two in the dog, while the arctic fox appeared to be monomorphic. In addition, association of several polymorphisms with body weight was analysed in red foxes (the number of genotyped animals ranged from 319 to 379). Two polymorphisms in the red fox, i.e. a silent substitution c.957A>C and c.*185C>T in the 3'-flanking sequence, showed a significant association (P < 0.01) with body weight. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

Y-Chromosome Markers for the Red Fox.

PubMed

Rando, Halie M; Stutchman, Jeremy T; Bastounes, Estelle R; Johnson, Jennifer L; Driscoll, Carlos A; Barr, Christina S; Trut, Lyudmila N; Sacks, Benjamin N; Kukekova, Anna V

2017-09-01

The de novo assembly of the red fox (Vulpes vulpes) genome has facilitated the development of genomic tools for the species. Efforts to identify the population history of red foxes in North America have previously been limited by a lack of information about the red fox Y-chromosome sequence. However, a megabase of red fox Y-chromosome sequence was recently identified over 2 scaffolds in the reference genome. Here, these scaffolds were scanned for repeated motifs, revealing 194 likely microsatellites. Twenty-three of these loci were selected for primer development and, after testing, produced a panel of 11 novel markers that were analyzed alongside 2 markers previously developed for the red fox from dog Y-chromosome sequence. The markers were genotyped in 76 male red foxes from 4 populations: 7 foxes from Newfoundland (eastern Canada), 12 from Maryland (eastern United States), and 9 from the island of Great Britain, as well as 48 foxes of known North American origin maintained on an experimental farm in Novosibirsk, Russia. The full marker panel revealed 22 haplotypes among these red foxes, whereas the 2 previously known markers alone would have identified only 10 haplotypes. The haplotypes from the 4 populations clustered primarily by continent, but unidirectional gene flow from Great Britain and farm populations may influence haplotype diversity in the Maryland population. The development of new markers has increased the resolution at which red fox Y-chromosome diversity can be analyzed and provides insight into the contribution of males to red fox population diversity and patterns of phylogeography. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Effect of C/N ratio on extracellular polymeric substances of activated sludge from an anoxic-aerobic sequencing batch reactor treating saline wastewater.

PubMed

Wang, Zichao; Gao, Mengchun; Xin, Yanjun; Ma, Dong; She, Zonglian; Wang, Zhe; Sun, Changqing; Ren, Yun

2014-01-01

The effect of C/N ratio on extracellular polymeric substances (EPS) of activated sludge was investigated in an anoxic-aerobic sequencing batch reactor (SBR) treating saline wastewater. The protein (PN) and protein/polysaccharide (PN/PS) ratio in the loosely bound EPS (LB-EPS) increased with the decrease of C/N ratio, whereas the PS in the LB-EPS decreased. The PS, PN and PN/PS ratio in the tightly bound EPS (TB-EPS) were independent of C/N ratio. Two fluorescence peaks in the LB-EPS and TB-EPS were identified at excitation/emission (Ex/Em) wavelengths of 275-280/335-340 nm and 220-225/330-340 nm by three-dimensional excitation-emission matrix (3D-EEM) fluorescence spectroscopy, respectively. These peaks in LB-EPS and TB-EPS were, respectively, associated with tryptophan protein-like substances and aromatic protein-like substances. The tryptophan protein-like fluorescence peaks in LB-EPS showed blue shift along the Ex axis and red shift along the Em axis with the decrease of C/N ratio. Fourier transform infrared spectra suggested that the variation of C/N ratio had more distinct effect on the functional groups of protein in the LB-EPS than those in the TB-EPS. The sludge volume index value decreased with the increase of LB-EPS, but there was no correlation between SVI and TB-EPS.

Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea

NASA Astrophysics Data System (ADS)

DiBattista, Joseph D.; Coker, Darren J.; Sinclair-Taylor, Tane H.; Stat, Michael; Berumen, Michael L.; Bunce, Michael

2017-12-01

Relatively small volumes of water may contain sufficient environmental DNA (eDNA) to detect target aquatic organisms via genetic sequencing. We therefore assessed the utility of eDNA to document the diversity of coral reef fishes in the central Red Sea. DNA from seawater samples was extracted, amplified using fish-specific 16S mitochondrial DNA primers, and sequenced using a metabarcoding workflow. DNA sequences were assigned to taxa using available genetic repositories or custom genetic databases generated from reference fishes. Our approach revealed a diversity of conspicuous, cryptobenthic, and commercially relevant reef fish at the genus level, with select genera in the family Labridae over-represented. Our approach, however, failed to capture a significant fraction of the fish fauna known to inhabit the Red Sea, which we attribute to limited spatial sampling, amplification stochasticity, and an apparent lack of sequencing depth. Given an increase in fish species descriptions, completeness of taxonomic checklists, and improvement in species-level assignment with custom genetic databases as shown here, we suggest that the Red Sea region may be ideal for further testing of the eDNA approach.

Using Green and Red Fluorescent Proteins to Teach Protein Expression, Purification, and Crystallization

ERIC Educational Resources Information Center

Wu, Yifeng; Zhou, Yangbin; Song, Jiaping; Hu, Xiaojian; Ding, Yu; Zhang, Zhihong

2008-01-01

We have designed a laboratory curriculum using the green and red fluorescent proteins (GFP and RFP) to visualize the cloning, expression, chromatography purification, crystallization, and protease-cleavage experiments of protein science. The EGFP and DsRed monomer (mDsRed)-coding sequences were amplified by PCR and cloned into pMAL (MBP-EGFP) or…

AT THE SOURCE OF AN EXTRAGALACTIC JET

NASA Technical Reports Server (NTRS)

2002-01-01

Artist's concept of the formation region of M87's jet. An accretion disk (red-yellow) surrounds the black hole, and its magnetic field lines twist tightly to channel the outpouring subatomic particles into a narrow jet. The jet opens widely near the black hole, then is shaped into a narrower beam within a light-year of the black hole. Credit: NASA and Ann Feild (Space Telescope Science Institute)

Molecular definition of red cell Rh haplotypes by tightly linked SphI RFLPs.

PubMed

Huang, C H; Reid, M E; Chen, Y; Coghlan, G; Okubo, Y

1996-01-01

The Rh blood group system of human red cells contains five major antigens D, C/c, and E/e (the latter four designated "non-D") that are specified by eight gene complexes known as Rh haplotypes. In this paper, we report on the mapping of RH locus and identification of a set of SphI RFLPs that are tightly linked with the Rh structural genes. Using exon-specific probes, we have localized the SphI cleavage sites resulting in these DNA markers and derived a comprehensive map for the RH locus. It was found that the SphI fragments encompassing exons 4-7 of the Rh genes occur in four banding patterns or frameworks that correspond to the distribution and segregation of the common Rh haplotypes. This linkage disequilibrium allowed a genotype-phenotype correlation and direct determination of Rh zygosity related to the Rh-positive or Rh-negative status (D/D, D/d, and d/d). Studies on the occurrence of SphI RFLPs in a number of rare Rh variants indicated that Rh phenotypic diversity has taken place on different haplotype backgrounds and has arisen by diverse genetic mechanisms. The molecular definition of Rh haplotypes by SphI RFLP frameworks should provide a useful procedure for genetic counseling and prenatal assessment of Rh alloimmunization.

Red, green, blue equals 1, 2, 3: Digit-color synesthetes can use structured digit information to boost recall of color sequences.

PubMed

Teichmann, A Lina; Nieuwenstein, Mark R; Rich, Anina N

2015-01-01

Digit-color synesthetes report experiencing colors when perceiving letters and digits. The conscious experience is typically unidirectional (e.g., digits elicit colors but not vice versa) but recent evidence shows subtle bidirectional effects. We examined whether short-term memory for colors could be affected by the order of presentation reflecting more or less structure in the associated digits. We presented a stream of colored squares and asked participants to report the colors in order. The colors matched each synesthete's colors for digits 1-9 and the order of the colors corresponded either to a sequence of numbers (e.g., [red, green, blue] if 1 = red, 2 = green, 3 = blue) or no systematic sequence. The results showed that synesthetes recalled sequential color sequences more accurately than pseudo-randomized colors, whereas no such effect was found for the non-synesthetic controls. Synesthetes did not differ from non-synesthetic controls in recall of color sequences overall, providing no evidence of a general advantage in memory for serial recall of colors.

Amelogenin Evolution and Tetrapod Enamel Structure

PubMed Central

Diekwisch, Thomas G.H.; Jin, Tianquan; Wang, Xinping; Ito, Yoshihiro; Schmidt, Marcella; Druzinsky, Robert; Yamane, Akira; Luan, Xianghong

2009-01-01

Amelogenins are the major proteins involved in tooth enamel formation. In the present study we have cloned and sequenced four novel amelogenins from three amphibian species in order to analyze similarities and differences between mammalian and non-mammalian amelogenins. The newly sequenced amphibian amelogenin sequences were from a Red-eyed tree frog (Litoria chloris) and a Mexican axolotl (Ambystoma mexicanum). We identified two amelogenin isoforms in the Eastern Red-backed Salamander (Plethodon cinereus). Sequence comparisons confirmed that non-mammalian amelogenins are overall shorter than their mammalian counterparts, contain less proline and less glutamine, and feature shorter polyproline tripeptide repeat stretches than mammalian amelogenins. We propose that unique sequence parameters of mammalian amelogenins might be a pre-requisite for complex mammalian enamel prism architecture. PMID:19828974

Colour variation in red grapevines (Vitis vinifera L.): genomic organisation, expression of flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase genes and related metabolite profiling of red cyanidin-/blue delphinidin-based anthocyanins in berry skin

PubMed Central

Castellarin, Simone D; Di Gaspero, Gabriele; Marconi, Raffaella; Nonis, Alberto; Peterlunger, Enrico; Paillard, Sophie; Adam-Blondon, Anne-Francoise; Testolin, Raffaele

2006-01-01

Background Structural genes of the phenyl-propanoid pathway which encode flavonoid 3'- and 3',5'-hydroxylases (F3'H and F3'5'H) have long been invoked to explain the biosynthesis of cyanidin- and delphinidin-based anthocyanin pigments in the so-called red cultivars of grapevine. The relative proportion of the two types of anthocyanins is largely under genetic control and determines the colour variation among red/purple/blue berry grape varieties and their corresponding wines. Results Gene fragments of VvF3'H and VvF3'5'H, that were isolated from Vitis vinifera 'Cabernet Sauvignon' using degenerate primers designed on plant homologous genes, translated into 313 and 239 amino acid protein fragments, respectively, with up to 76% and 82% identity to plant CYP75 cytochrome P450 monooxygenases. Putative function was assigned on the basis of sequence homology, expression profiling and its correlation with metabolite accumulation at ten different ripening stages. At the onset of colour transition, transcriptional induction of VvF3'H and VvF3'5'H was temporally coordinated with the beginning of anthocyanin biosynthesis, the expression being 2-fold and 50-fold higher, respectively, in red berries versus green berries. The peak of VvF3'5'H expression was observed two weeks later concomitantly with the increase of the ratio of delphinidin-/cyanidin-derivatives. The analysis of structural genomics revealed that two copies of VvF3'H are physically linked on linkage group no. 17 and several copies of VvF3'5'H are tightly clustered and embedded into a segmental duplication on linkage group no. 6, unveiling a high complexity when compared to other plant flavonoid hydroxylase genes known so far, mostly in ornamentals. Conclusion We have shown that genes encoding flavonoid 3'- and 3',5'-hydroxylases are expressed in any tissues of the grape plant that accumulate flavonoids and, particularly, in skin of ripening red berries that synthesise mostly anthocyanins. The correlation between transcript profiles and the kinetics of accumulation of red/cyanidin- and blue/delphinidin-based anthocyanins indicated that VvF3'H and VvF3'5'H expression is consistent with the chromatic evolution of ripening bunches. Local physical maps constructed around the VvF3'H and VvF3'5'H loci should help facilitate the identification of the regulatory elements of each isoform and the future manipulation of grapevine and wine colour through agronomical, environmental and biotechnological tools. PMID:16433923

Tightness of the Ising-Kac Model on the Two-Dimensional Torus

NASA Astrophysics Data System (ADS)

Hairer, Martin; Iberti, Massimo

2018-05-01

We consider the sequence of Gibbs measures of Ising models with Kac interaction defined on a periodic two-dimensional discrete torus near criticality. Using the convergence of the Glauber dynamic proven by Mourrat and Weber (Commun Pure Appl Math 70:717-812, 2017) and a method by Tsatsoulis and Weber employed in (arXiv:1609.08447 2016), we show tightness for the sequence of Gibbs measures of the Ising-Kac model near criticality and characterise the law of the limit as the Φ ^4_2 measure on the torus. Our result is very similar to the one obtained by Cassandro et al. (J Stat Phys 78(3):1131-1138, 1995) on Z^2, but our strategy takes advantage of the dynamic, instead of correlation inequalities. In particular, our result covers the whole critical regime and does not require the large temperature/large mass/small coupling assumption present in earlier results.

[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).

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

A Policy and Program for Invigorating Science and Technology for National Security

DTIC Science & Technology

2014-04-01

technical support – academia competes against industry often appearing as cheap labour but then without generating commercially viable or sustainable...have new technology approved too bureaucratic keeping SME’s out of the market DSTO provide greater transparency of S&T goals to enable industry to...national security S&T. In endeavouring to meet the Government’s desire to reduce red tape and cognisant of the tight financial environment, consideration

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.

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.

Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan

PubMed Central

Chen, Yue; Hora, Bhavna; DeMarco, Todd; Shah, Sharaf Ali; Ahmed, Manzoor; Sanchez, Ana M.; Su, Chang; Carter, Meredith; Stone, Mars; Hasan, Rumina; Hasan, Zahra; Busch, Michael P.; Denny, Thomas N.; Gao, Feng

2016-01-01

A number of HIV-1 subtypes are identified in Pakistan by characterization of partial viral gene sequences. Little is known whether new recombinants are generated and how they disseminate since whole genome sequences for these viruses have not been characterized. Near full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes or next generation sequencing from 34 HIV-1-infected individuals in Pakistan. Phylogenetic tree analysis showed that the newly characterized sequences were 16 subtype As, one subtype C, and 17 A/G recombinants. Further analysis showed that all 16 subtype A1 sequences (47%), together with the vast majority of sequences from Pakistan from other studies, formed a tight subcluster (A1a) within the subtype A1 clade, suggesting that they were derived from a single introduction. More in-depth analysis of 17 A/G NFLG sequences showed that five shared similar recombination breakpoints as in CRF02 (15%) but were phylogenetically distinct from the prototype CRF02 by forming a tight subcluster (CRF02a) while 12 (38%) were new recombinants between CRF02a and A1a or a divergent A1b viruses. Unique recombination patterns among the majority of the newly characterized recombinants indicated ongoing recombination. Interestingly, recombination breakpoints in these CRF02/A1 recombinants were similar to those in prototype CRF02 viruses, indicating that recombination at these sites more likely generate variable recombinant viruses. The dominance and fast dissemination of new CRF02a/A1 recombinants over prototype CRF02 suggest that these recombinant have more adapted and may become major epidemic strains in Pakistan. PMID:27973597

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.

The evolution of the cluster optical galaxy luminosity function between z = 0.4 and 0.9 in the DAFT/FADA survey

NASA Astrophysics Data System (ADS)

Martinet, Nicolas; Durret, Florence; Guennou, Loïc; Adami, Christophe; Biviano, Andrea; Ulmer, Melville P.; Clowe, Douglas; Halliday, Claire; Ilbert, Olivier; Márquez, Isabel; Schirmer, Mischa

2015-03-01

Context. There is some disagreement about the abundance of faint galaxies in high-redshift clusters, with contradictory results in the literature arising from studies of the optical galaxy luminosity function (GLF) for small cluster samples. Aims: We compute GLFs for one of the largest medium-to-high-redshift (0.4 ≤ z < 0.9) cluster samples to date in order to probe the abundance of faint galaxies in clusters. We also study how the GLF depends on cluster redshift, mass, and substructure and compare the GLFs of clusters with those of the field. We separately investigate the GLFs of blue and red-sequence (RS) galaxies to understand the evolution of different cluster populations. Methods: We calculated the GLFs for 31 clusters taken from the DAFT/FADA survey in the B,V,R, and I rest-frame bands. We used photometric redshifts computed from BVRIZJ images to constrain galaxy cluster membership. We carried out a detailed estimate of the completeness of our data. We distinguished the red-sequence and blue galaxies using a V - I versus I colour-magnitude diagram. We studied the evolution of these two populations with redshift. We fitted Schechter functions to our stacked GLFs to determine average cluster characteristics. Results: We find that the shapes of our GLFs are similar for the B,V,R, and I bands with a drop at the red GLF faint ends that is more pronounced at high redshift: αred ~ -0.5 at 0.40 ≤ z < 0.65 and αred > 0.1 at 0.65 ≤ z < 0.90. The blue GLFs have a steeper faint end (αblue ~ -1.6) than the red GLFs, which appears to be independent of redshift. For the full cluster sample, blue and red GLFs meet at MV = -20, MR = -20.5, and MI = -20.3. A study of how galaxy types evolve with redshift shows that late-type galaxies appear to become early types between z ~ 0.9 and today. Finally, the faint ends of the red GLFs of more massive clusters appear to be richer than less massive clusters, which is more typical of the lower redshift behaviour. Conclusions: Our results indicate that these clusters form at redshifts higher than z = 0.9 from galaxy structures that already have an established red sequence. Late-type galaxies then appear to evolve into early types, enriching the red sequence between this redshift and today. This effect is consistent with the evolution of the faint-end slope of the red sequence and the galaxy type evolution that we find. Finally, faint galaxies accreted from the field environment at all redshifts might have replaced the blue late-type galaxies that converted into early types, explaining the lack of evolution in the faint-end slopes of the blue GLFs. Appendix is available in electronic form at http://www.aanda.org

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.

Stromal characterization and comparison of odontogenic cysts and odontogenic tumors using picrosirius red stain and polarizing microscopy: A retrospective and histochemical study.

PubMed

Jahagirdar, P B; Kale, A D; Hallikerimath, S

2015-01-01

Odontogenic lesions represent a range of conditions, the features of which probably depend on the stage of induction towards tooth formation reached prior to neoplastic or hamartomatous proliferation. It has been also suggested that inductive changes may allow progression from one type of odontogenic tumor to another. The epithelium also plays an important role in the pathogenesis of these lesions; even stroma is likely to play an equally important role in the pathogenesis and biological behavior. So, this study was performed to investigate, compare, and correlate different types of collagen fibers in odontogenic cysts and odontogenic tumors. Thirty each pre-diagnosed odontogenic cysts and tumors were histochemically analyzed using a special stain (Picrosirius red stain) and polarizing microscopy. Seven cases (99%) of inflammatory cysts exhibited predominantly greenish-yellow birefringence indicating procollagen, intermediate, or pathologic collagen fibers suggestive of loosely packed collagen fibers. Predominant yellowish-orange birefringence exhibited by 21 cases (99%) of developmental cysts was comparable to the yellowish-orange and orangish-red to red birefringence exhibited by odontogenic tumors suggesting tightly packed fibers. The Picrosirius red stain in conjunction with polarizing microscopy serves as a specific and sensitive tool in characterizing collagen fibers in odontogenic cysts and odontogenic tumor.

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.

High-throughput linear optical stretcher for mechanical characterization of blood cells.

PubMed

Roth, Kevin B; Neeves, Keith B; Squier, Jeff; Marr, David W M

2016-04-01

This study describes a linear optical stretcher as a high-throughput mechanical property cytometer. Custom, inexpensive, and scalable optics image a linear diode bar source into a microfluidic channel, where cells are hydrodynamically focused into the optical stretcher. Upon entering the stretching region, antipodal optical forces generated by the refraction of tightly focused laser light at the cell membrane deform each cell in flow. Each cell relaxes as it flows out of the trap and is compared to the stretched state to determine deformation. The deformation response of untreated red blood cells and neutrophils were compared to chemically treated cells. Statistically significant differences were observed between normal, diamide-treated, and glutaraldehyde-treated red blood cells, as well as between normal and cytochalasin D-treated neutrophils. Based on the behavior of the pure, untreated populations of red cells and neutrophils, a mixed population of these cells was tested and the discrete populations were identified by deformability. © 2015 International Society for Advancement of Cytometry. © 2015 International Society for Advancement of Cytometry.

Determination of Urea Permeability in Red Cells by Minimum Method

PubMed Central

Sha'afi, R. I.; Rich, G. T.; Mikulecky, D. C.; Solomon, A. K.

1970-01-01

A new method has been developed for measuring the permeability coefficient, ω, of small nonelectrolytes. The method depends upon a mathematical analysis of the time course of cell volume changes in the neighborhood of the minimum volume following addition of a permeating solute to an isosmolal buffer. Coefficients determined by the minimum volume method agree with those obtained using radioactive tracers. ω for urea in human red cells was found to decrease as the volume flow, Jv, into the cell increased. Such behavior is entirely unexpected for a single uniform rate-limiting barrier on the basis of the linear phenomenological equations derived from irreversible thermodynamics. However, the present findings are consonant with a complex membrane system consisting of a tight barrier on the outer face of the human red cell membrane and a somewhat less restrictive barrier behind it closer to the inner membrane face. A theoretical analysis of such a series model has been made which makes predictions consistent with the experimental findings. PMID:5435779

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.

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.

Insertion of a solo LTR retrotransposon associates with spur mutations in 'Red Delicious' apple (Malus × domestica).

PubMed

Han, Mengxue; Sun, Qibao; Zhou, Junyong; Qiu, Huarong; Guo, Jing; Lu, Lijuan; Mu, Wenlei; Sun, Jun

2017-09-01

Insertion of a solo LTR, which possesses strong bidirectional, stem-specific promoter activities, is associated with the evolution of a dwarfing apple spur mutation. Spur mutations in apple scions revolutionized global apple production. Since long terminal repeat (LTR) retrotransposons are tightly related to natural mutations, inter-retrotransposon-amplified polymorphism technique and genome walking were used to find sequences in the apple genome based on these LTRs. In 'Red Delicious' spur mutants, a novel, 2190-bp insertion was identified as a spur-specific, solo LTR (sLTR) located at the 1038th nucleotide of another sLTR, which was 1536 bp in length. This insertion-within-an-insertion was localized within a preexisting Gypsy-50 retrotransposon at position 3,762,767 on chromosome 4. The analysis of transcriptional activity of the two sLTRs (the 2190- and 1536-bp inserts) indicated that the 2190-bp sLTR is a promoter, capable of bidirectional transcription. GUS expression in the 2190-bp-sense and 2190-bp-antisense transgenic lines was prominent in stems. In contrast, no promoter activity from either the sense or the antisense strand of the 1536-bp sLTR was detected. From ~150 kb of DNA on each side of the 2190 bp, sLTR insertion site, corresponding to 300 kb of the 'Golden Delicious' genome, 23 genes were predicted. Ten genes had predicted functions that could affect shoot development. This first report, of a sLTR insertion associated with the evolution of apple spur mutation, will facilitate apple breeding, cloning of spur-related genes, and discovery of mechanisms behind dwarf habit.

Personal Protective Equipment Guide for Military Medical Treatment Facility Personnel Handling Casualties From Weapons of Mass Destruction and Terrorism Events

DTIC Science & Technology

2003-08-01

nearly 100% unless it is treated within 18 hours. • Tularemia: ulceroglandular tularemia presents with a local ulcer and regional lymph node...Ref. 48): acute onset of fever, chest tightness, cough, labored or difficult breathing, nausea, and joint pains. Airway necrosis and pulmonary...redness, vesicles, necrosis and sloughing of the epidermis. Effects on the airway include nose and throat pain, nasal discharge, itching and

Molecular definition of red cell Rh haplotypes by tightly linked SphI RFLPs

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

Huang, C.H.; Reid, M.E.; Chen, Y.

The Rh blood group system of human red cells contains five major antigens D, C/c, and E/e (the latter four designated {open_quotes}non-D{close_quotes}) that are specified by eight gene complexes known as Rh haplotypes. In this paper, we report on the mapping of the RH locus and identification of a set of SphI RFLPs that are tightly linked with the Rh structural genes. Using exon-specific probes, we have localized the SphI cleavage sites resulting in these DNA markers and derived a comprehensive map for the RH locus. It was found that the SphI fragments encompassing exons 4-7 of the Rh genesmore » occur in four banding patterns or frameworks that correspond to the distribution and segregation of the common Rh haplotypes. This linkage disequilibrium allowed a genotype-phenotype correlation and direct determination of Rh zygosity related to the Rh-positive or Rh-negative status (D/D, D/d, and d/d). Studies on the occurrence of SphI RFLPs in a number of rare Rh variants indicated that Rh phenotypic diversity has taken place on different haplotype backgrounds and has arisen by diverse genetic mechanisms. The molecular definition of Rh haplotypes by SphI RFLP frameworks should provide a useful procedure for genetic counseling and prenatal assessment of Rh alloimmunization. 32 refs., 7 figs., 3 tabs.« less

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.

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...

Interaction between bending and tension forces in bilayer membranes.

PubMed Central

Secomb, T W

1988-01-01

A theoretical analysis is presented of the bending mechanics of a membrane consisting of two tightly-coupled leaflets, each of which shears and bends readily but strongly resists area changes. Structures of this type have been proposed to model biological membranes such as red blood cell membrane. It is shown that when such a membrane is bent, anisotropic components of resultant membrane tension (shear stresses) are induced, even when the tension in each leaflet is isotropic. The induced shear stresses increase as the square of the membrane curvature, and become significant for moderate curvatures (when the radius of curvature is much larger than the distance between the leaflets). This effect has implications for the analysis of shape and deformation of freely suspended and flowing red blood cells. PMID:3224154

The thrust belt in Southwest Montana and east-central Idaho

USGS Publications Warehouse

Ruppel, Edward T.; Lopez, David A.

1984-01-01

The leading edge of the Cordilleran fold and thrust in southwest Montana appears to be a continuation of the edge of the Wyoming thrust belt, projected northward beneath the Snake River Plain. Trces of the thrust faults that form the leading edge of the thrust belts are mostly concealed, but stratigraphic and structural evidence suggests that the belt enters Montana near the middle of the Centennial Mountains, continues west along the Red Rock River valley, and swings north into the Highland Mountains near Butte. The thrust belt in southwest Montana and east-central Idaho includes at least two major plates -- the Medicine Lodge and Grasshopper thrust plates -- each of which contains a distinctive sequence of rocks, different in facies and structural style from those of the cratonic region east of the thrust belt. The thrust plates are characterized by persuasive, open to tight and locally overturned folds, and imbricate thrust faults, structural styles unusual in Phanerozoic cratonic rocks. The basal decollement zones of the plates are composed of intensely sheared, crushed, brecciated, and mylonitized rocks, the decollement at the base of the Medicine Lodge plate is as much as 300 meters thick. The Medicine Lodge and Grasshopper thrust plates are fringed on the east by a 10- to 50-kilometer-wide zone of tightly folded rocks cut by imbricate thrust fauls, a zone that forms the eastern margin of the thrust belt in southwest Montana. The frontal fold and thrust zone includes rocks that are similar to those of the craton, even though they differ in details of thickness, composition, or stratigraphic sequence. The zone is interpreted to be one of terminal folding and thrusting in cratonic rocks overridden by the major thrust plates from farther west. The cratonic rocks were drape-folded over rising basement blocks that formed a foreland bulge in front of the thrust belt. The basement blocks are bounded by steep faults of Proterozoic ancestry, which also moved as tear faults during thrusting, and seem to have controlled the curving patterns of salients and reentrants at the leading edge of the thrust belt. Radiometric and stratiographic evidence shows that the thrust belt was in its present position by about 75 million year go.

Textural and mineralogical study of sandstones from the onshore Gulf of Alaska Tertiary Province, southern Alaska

USGS Publications Warehouse

Winkler, Gary R.; McLean, Hugh; Plafker, George

1976-01-01

Petrographic examination of 74 outcrop samples of Paleocene through Pliocene age from the onshore Gulf of Alaska Tertiary Province indicates that sandstones of the province characteristically are texturally immature and mineralogically unstable. Diagenetic alteration of framework grains throughout the stratigraphic sequence has produced widespread zeolite cement or phyllosilicate grain coatings and pseudomatrix. Multiple deformation and deep burial of the older Tertiary sequence--the Orca Group, the shale of Haydon Peak, and the Kulthieth and Tokun Formations--caused extensive alteration and grain interpenetration, resulting in low porosity values. Less intense deformation and intermediate depth of burial of the younger Tertiary sequence--the Katalla, Poul Creek, Redwood, and Yakataga Formations--has resulted in a greater range in textural properties. Most sandstone samples in the younger Tertiary sequence are poorly sorted, tightly packed, and have strongly appressed framework grains, but some are less tightly packed and contain less matrix. Soft and mineralogically unstable framework grains have undergone considerable alteration, reducing pore space even in the youngest rocks. Measurements of porosity, permeability, grain density, and sonic velocity of outcrop samples of the younger Tertiary sequence indicate a modest up-section improvement in sandstone reservoir characteristics. Nonetheless porosity and permeability values typically are below 16 percent and 15 millidarcies respectively and grain densities are consistently high, about 2.7 gm/cc. Low permeability and porosity values, and high grain densities and sonic velocities appear to be typical of most outcrop areas throughout the onshore Gulf of Alaska Tertiary Province.

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...

Reported respiratory symptom intensity in asthmatics during exposure to aerosolized Florida red tide toxins.

PubMed

Milian, Alexyz; Nierenberg, Kate; Fleming, Lora E; Bean, Judy A; Wanner, Adam; Reich, Andrew; Backer, Lorraine C; Jayroe, David; Kirkpatrick, Barbara

2007-09-01

Florida red tides are naturally occurring blooms of the marine dinoflagellate, Karenia brevis. K. brevis produces natural toxins called brevetoxins. Brevetoxins become part of the marine aerosol as the fragile, unarmored cells are broken up by wave action. Inhalation of the aerosolized toxin results in upper and lower airway irritation. Symptoms of brevetoxin inhalation include: eye, nose, and throat irritation, coughing, wheezing, chest tightness, and shortness of breath. Asthmatics appear to be more sensitive to the effects of inhaled brevetoxin. This study examined data from 97 asthmatics exposed at the beach for 1 hour during K. brevis blooms, and on separate occasions when no bloom was present. In conjunction with extensive environmental monitoring, participants were evaluated utilizing questionnaires and pulmonary function testing before and after a 1-hour beach walk. A modified Likert scale was incorporated into the questionnaire to create respiratory symptom intensity scores for each individual pre- and post-beach walk. Exposure to Florida red tide significantly increased the reported intensity of respiratory symptoms; no significant changes were seen during an unexposed period. This is the first study to examine the intensity of reported respiratory symptoms in asthmatics after a 1-hour exposure to Florida red tide.

Reported Respiratory Symptom Intensity in Asthmatics During Exposure to Aerosolized Florida Red Tide Toxins

PubMed Central

Milian, Alexyz; Nierenberg, Kate; Fleming, Lora E.; Bean, Judy A.; Wanner, Adam; Reich, Andrew; Backer, Lorraine C.; Jayroe, David; Kirkpatrick, Barbara

2010-01-01

Florida red tides are naturally occurring blooms of the marine dinoflagellate, Karenia brevis. K. brevis produces natural toxins called brevetoxins. Brevetoxins become part of the marine aerosol as the fragile, unarmored cells are broken up by wave action. Inhalation of the aerosolized toxin results in upper and lower airway irritation. Symptoms of brevetoxin inhalation include: eye, nose, and throat irritation, coughing, wheezing, chest tightness, and shortness of breath. Asthmatics appear to be more sensitive to the effects of inhaled brevetoxin. This study examined data from 97 asthmatics exposed at the beach for 1 hour during K. brevis blooms, and on separate occasions when no bloom was present. In conjunction with extensive environmental monitoring, participants were evaluated utilizing questionnaires and pulmonary function testing before and after a 1-hour beach walk. A modified Likert scale was incorporated into the questionnaire to create respiratory symptom intensity scores for each individual pre- and post-beach walk. Exposure to Florida red tide significantly increased the reported intensity of respiratory symptoms; no significant changes were seen during an unexposed period. This is the first study to examine the intensity of reported respiratory symptoms in asthmatics after a 1-hour exposure to Florida red tide. PMID:17885863

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.

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.

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.

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.

Nucleotide sequence of a cluster of early and late genes in a conserved segment of the vaccinia virus genome.

PubMed Central

Plucienniczak, A; Schroeder, E; Zettlmeissl, G; Streeck, R E

1985-01-01

The nucleotide sequence of a 7.6 kb vaccinia DNA segment from a genomic region conserved among different orthopox virus has been determined. This segment contains a tight cluster of 12 partly overlapping open reading frames most of which can be correlated with previously identified early and late proteins and mRNAs. Regulatory signals used by vaccinia virus have been studied. Presumptive promoter regions are rich in A, T and carry the consensus sequences TATA and AATAA spaced at 20-24 base pairs. Tandem repeats of a CTATTC consensus sequence are proposed to be involved in the termination of early transcription. PMID:2987815

Nocardioides rubroscoriae sp. nov., isolated from volcanic ash.

PubMed

Lee, Soon Dong; Lee, Dong Wan

2014-06-01

A rod-shaped actinobacterium, designated Sco-A25(T), was isolated from a red-coloured layer of scoria (volcanic ash) in the Republic of Korea and subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain Sco-A25(T) is a member of the genus Nocardioides and formed a tight monophyletic unit with the type strain of Nocardioides plantarum (98.7 % gene similarity). LL-Diaminopimelic acid was detected in the cell wall. The predominant menaquinone is MK-8(H4). The polar lipids found were phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, and an unknown phospholipid. The fatty acid profile was represented by large amounts of saturated, unsaturated and iso-branched fatty acids. The DNA G+C content was 71.6 mol %. Genomic DNA similarity between strain Sco-A25(T) and N. plantarum KCTC 9577(T) was 47.8 %. On the basis of the results of phenotypic, genetic and phylogenetic analyses presented here, strain Sco-A25(T) is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides rubroscoriae sp. nov. is proposed. The type strain is Sco-A25(T) (=KCTC 19805(T) = DSM 23986(T) = NBRC 107916(T)).

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.

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.

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

Molecular Population Genetics of the Alcohol Dehydrogenase Gene Region of DROSOPHILA MELANOGASTER

PubMed Central

Aquadro, Charles F.; Desse, Susan F.; Bland, Molly M.; Langley, Charles H.; Laurie-Ahlberg, Cathy C.

1986-01-01

Variation in the DNA restriction map of a 13-kb region of chromosome II including the alcohol dehydrogenase structural gene (Adh) was examined in Drosophila melanogaster from natural populations. Detailed analysis of 48 D. melanogaster lines representing four eastern United States populations revealed extensive DNA sequence variation due to base substitutions, insertions and deletions. Cloning of this region from several lines allowed characterization of length variation as due to unique sequence insertions or deletions [nine sizes; 21–200 base pairs (bp)] or transposable element insertions (several sizes, 340 bp to 10.2 kb, representing four different elements). Despite this extensive variation in sequences flanking the Adh gene, only one length polymorphism is clearly associated with altered Adh expression (a copia element approximately 250 bp 5' to the distal transcript start site). Nonetheless, the frequency spectra of transposable elements within and between Drosophila species suggests they are slightly deleterious. Strong nonrandom associations are observed among Adh region sequence variants, ADH allozyme (Fast vs. Slow), ADH enzyme activity and the chromosome inversion ln(2L) t. Phylogenetic analysis of restriction map haplotypes suggest that the major twofold component of ADH activity variation (high vs. low, typical of Fast and Slow allozymes, respectively) is due to sequence variation tightly linked to and possibly distinct from that underlying the allozyme difference. The patterns of nucleotide and haplotype variation for Fast and Slow allozyme lines are consistent with the recent increase in frequency and spread of the Fast haplotype associated with high ADH activity. These data emphasize the important role of evolutionary history and strong nonrandom associations among tightly linked sequence variation as determinants of the patterns of variation observed in natural populations. PMID:3026893

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

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 ...

Resonant-enhanced full-color emission of quantum-dot-based micro LED display technology.

PubMed

Han, Hau-Vei; Lin, Huang-Yu; Lin, Chien-Chung; Chong, Wing-Cheung; Li, Jie-Ru; Chen, Kuo-Ju; Yu, Peichen; Chen, Teng-Ming; Chen, Huang-Ming; Lau, Kei-May; Kuo, Hao-Chung

2015-12-14

Colloidal quantum dots which can emit red, green, and blue colors are incorporated with a micro-LED array to demonstrate a feasible choice for future display technology. The pitch of the micro-LED array is 40 μm, which is sufficient for high-resolution screen applications. The method that was used to spray the quantum dots in such tight space is called Aerosol Jet technology which uses atomizer and gas flow control to obtain uniform and controlled narrow spots. The ultra-violet LEDs are used in the array to excite the red, green and blue quantum dots on the top surface. To increase the utilization of the UV photons, a layer of distributed Bragg reflector was laid down on the device to reflect most of the leaked UV photons back to the quantum dot layers. With this mechanism, the enhanced luminous flux is 194% (blue), 173% (green) and 183% (red) more than that of the samples without the reflector. The luminous efficacy of radiation (LER) was measured under various currents and a value of 165 lm/Watt was recorded.

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.

OBSERVATIONAL CONSTRAINTS ON RED AND BLUE HELIUM BURNING SEQUENCES

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

McQuinn, Kristen B. W.; Skillman, Evan D.; Dalcanton, Julianne J.

We derive the optical luminosity, colors, and ratios of the blue and red helium burning (HeB) stellar populations from archival Hubble Space Telescope observations of nineteen starburst dwarf galaxies and compare them with theoretical isochrones from Padova stellar evolution models across metallicities from Z = 0.001 to 0.009. We find that the observational data and the theoretical isochrones for both blue and red HeB populations overlap in optical luminosities and colors and the observed and predicted blue to red HeB ratios agree for stars older than 50 Myr over the time bins studied. These findings confirm the usefulness of applyingmore » isochrones to interpret observations of HeB populations. However, there are significant differences, especially for the red HeB population. Specifically, we find (1) offsets in color between the observations and theoretical isochrones of order 0.15 mag (0.5 mag) for the blue (red) HeB populations brighter than M{sub V} {approx} -4 mag, which cannot be solely due to differential extinction; (2) blue HeB stars fainter than M{sub V} {approx} -3 mag are bluer than predicted; (3) the slope of the red HeB sequence is shallower than predicted by a factor of {approx}3; and (4) the models overpredict the ratio of the most luminous blue to red HeB stars corresponding to ages {approx}< 50 Myr. Additionally, we find that for the more metal-rich galaxies in our sample (Z {approx}> 0.5 Z{sub sun}), the red HeB stars overlap with the red giant branch stars in the color-magnitude diagrams, thus reducing their usefulness as indicators of star formation for ages {approx}> 100 Myr.« less

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.

Temporal Sequence of Cell Wall Disassembly in Rapidly Ripening Melon Fruit1

PubMed Central

Rose, Jocelyn K.C.; Hadfield, Kristen A.; Labavitch, John M.; Bennett, Alan B.

1998-01-01

The Charentais variety of melon (Cucumis melo cv Reticulatus F1 Alpha) was observed to undergo very rapid ripening, with the transition from the preripe to overripe stage occurring within 24 to 48 h. During this time, the flesh first softened and then exhibited substantial disintegration, suggesting that Charentais may represent a useful model system to examine the temporal sequence of changes in cell wall composition that typically take place in softening fruit. The total amount of pectin in the cell wall showed little reduction during ripening but its solubility changed substantially. Initial changes in pectin solubility coincided with a loss of galactose from tightly bound pectins, but preceded the expression of polygalacturonase (PG) mRNAs, suggesting early, PG-independent modification of pectin structure. Depolymerization of polyuronides occurred predominantly in the later ripening stages, and after the appearance of PG mRNAs, suggesting the existence of PG-dependent pectin degradation in later stages. Depolymerization of hemicelluloses was observed throughout ripening, and degradation of a tightly bound xyloglucan fraction was detected at the early onset of softening. Thus, metabolism of xyloglucan that may be closely associated with cellulose microfibrils may contribute to the initial stages of fruit softening. A model is presented of the temporal sequence of cell wall changes during cell wall disassembly in ripening Charentais melon. PMID:9625688

Parasitic nematodes of the genus Syphacia Seurat, 1916 infecting Muridae in the British Isles, and the peculiar case of Syphacia frederici.

PubMed

Stewart, Alex; Lowe, Ann; Smales, Lesley; Bajer, Anna; Bradley, Jan; Dwużnik, Dorota; Franssen, Frits; Griffith, Jack; Stuart, Peter; Turner, Cyan; Zaleśny, Grzegorz; Behnke, Jerzy M

2018-03-01

Syphacia stroma (von Linstow, 1884) Morgan, 1932 and Syphacia frederici Roman, 1945 are oxyurid nematodes that parasitize two murid rodents, Apodemus sylvaticus and Apodemus flavicollis, on the European mainland. Only S. stroma has been recorded previously in Apodemus spp. from the British Isles. Despite the paucity of earlier reports, we identified S. frederici in four disparate British sites, two in Nottinghamshire, one each in Berkshire and Anglesey, Wales. Identification was based on their site in the host (caecum and not small intestine), on key morphological criteria that differentiate this species from S. stroma (in particular the tail of female worms) and by sequencing two genetic loci (cytochrome C oxidase 1 gene and a section of ribosomal DNA). Sequences derived from both genetic loci of putative British S. frederici isolates formed a tight clade with sequences from continental worms known to be S. frederici, clearly distinguishing these isolates from S. stroma which formed a tight clade of its own, distinct from clades representative of Syphacia obvelata from Mus and S. muris from Rattus. The data in this paper therefore constitute the first record of S. frederici from British wood mice, and confirm the status of this species as distinct from both S. obvelata and S. stroma.

[Study on shape and structure of calcified cartilage zone in normal human knee joint].

PubMed

Wang, Fuyou; Yang, Liu; Duan, Xiaojun; Tan, Hongbo; Dai, Gang

2008-05-01

To explore the shape and structure of calcified cartilage zone and its interface between the non-calcified articular cartilage and subchondral bone plate. The normal human condyles of femur (n=20) were obtained from the tissue bank donated by the residents, 10 males and 10 females, aged 17-45 years. The longitudinal and transverse paraffin sections were prepared by the routine method. The shape and structure of calcified cartilage zone were observed with the Safranin O/fast green and von kossa stain method. The interface conjunction among zones of cartilage was researched by SEM and the 3D structural model was established by serial sections and modeling technique. Articular bone-cartilage safranin O/fast green staining showed that cartilage was stained red and subchondral bone was stained blue. The calcified cartilage zone was located between the tidemark and cement line. Von kossa staining showed that calcified cartilage zone was stained black and sharpness of structure border. Upper interface gomphosised tightly with the non-calcified cartilage by the wave shaped tidemark and lower interface anchored tightly with the subchondral bone by the uneven comb shaped cement line. The non-calcified cartilage zone was interlocked tightly in the manner of "ravine-engomphosis" by the calcified cartilage zone as observed under SEM, and the subchondral bone was anchored tightly in the manner of"comb-anchor" by the in the calcified cartilage zone 3D reconstruction model. The calcified cartilage zone is an important structure in the articular cartilage. The articular cartilage is fixed firmly into subchondral bone plate by the distinctive conjunct interfaces of calcified cartilage zone.

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.

Mechanism of red mud combined with Fenton's reagent in sewage sludge conditioning.

PubMed

Zhang, Hao; Yang, Jiakuan; Yu, Wenbo; Luo, Sen; Peng, Li; Shen, Xingxing; Shi, Yafei; Zhang, Shinan; Song, Jian; Ye, Nan; Li, Ye; Yang, Changzhu; Liang, Sha

2014-08-01

Red mud was evaluated as an alternative skeleton builder combined with Fenton's reagent in sewage sludge conditioning. The results show that red mud combined with Fenton's reagent showed good conditioning capability with the pH of the filtrate close to neutrality, indicating that red mud acted as a neutralizer as well as a skeleton builder when jointly used with Fenton's reagent. Through response surface methodology (RSM), the optimal dosages of Fe(2+), H2O2 and red mud were proposed as 31.9, 33.7 and 275.1 mg/g DS (dry solids), respectively. The mechanism of the composite conditioner could be illuminated as follows: (1) extracellular polymeric substances (EPS), including loosely bound EPS and tightly bound EPS, were degraded into dissolved organics, e.g., proteins and polysaccharides; (2) bound water was released and converted into free water due to the degradation of EPS; and (3) morphology of the conditioned sludge exhibited a porous structure in contrast with the compact structure of raw sludge, and the addition of red mud formed new mineral phases and a rigid lattice structure in sludge, allowing the outflow of free water. Thus, sludge dewatering performance was effectively improved. The economic assessment for a wastewater treatment plant of 370,000 equivalent inhabitants confirms that using red mud conditioning, combined with Fenton's reagent, leads to a saving of approximately 411,000 USD/y or 50.8 USD/t DS comparing with using lime and ordinary Portland cement combined with Fenton's reagent, and approximately 612,000 USD/y or 75.5 USD/t DS comparing with the traditional treatment. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparative population genetics of a mimicry locus among hybridizing Heliconius butterfly species.

PubMed

Chamberlain, N L; Hill, R I; Baxter, S W; Jiggins, C D; Kronforst, M R

2011-09-01

The comimetic Heliconius butterfly species pair, H. erato and H. melpomene, appear to use a conserved Mendelian switch locus to generate their matching red wing patterns. Here we investigate whether H. cydno and H. pachinus, species closely related to H. melpomene, use this same switch locus to generate their highly divergent red and brown color pattern elements. Using an F2 intercross between H. cydno and H. pachinus, we first map the genomic positions of two novel red/brown wing pattern elements; the G locus, which controls the presence of red vs brown at the base of the ventral wings, and the Br locus, which controls the presence vs absence of a brown oval pattern on the ventral hind wing. The results reveal that the G locus is tightly linked to markers in the genomic interval that controls red wing pattern elements of H. erato and H. melpomene. Br is on the same linkage group but approximately 26 cM away. Next, we analyze fine-scale patterns of genetic differentiation and linkage disequilibrium throughout the G locus candidate interval in H. cydno, H. pachinus and H. melpomene, and find evidence for elevated differentiation between H. cydno and H. pachinus, but no localized signature of association. Overall, these results indicate that the G locus maps to the same interval as the locus controlling red patterning in H. melpomene and H. erato. This, in turn, suggests that the genes controlling red pattern elements may be homologous across Heliconius, supporting the hypothesis that Heliconius butterflies use a limited suite of conserved genetic switch loci to generate both convergent and divergent wing patterns.

A multi-wavelength study of the evolution of early-type galaxies in groups: the ultraviolet view

NASA Astrophysics Data System (ADS)

Rampazzo, R.; Mazzei, P.; Marino, A.; Bianchi, L.; Plana, H.; Trinchieri, G.; Uslenghi, M.; Wolter, A.

2018-04-01

The ultraviolet-optical colour magnitude diagram of rich galaxy groups is characterised by a well developed Red Sequence, a Blue Cloud and the so-called Green Valley. Loose, less evolved groups of galaxies which are probably not virialised yet may lack a well defined Red Sequence. This is actually explained in the framework of galaxy evolution. We are focussing on understanding galaxy migration towards the Red Sequence, checking for signatures of such a transition in their photometric and morphological properties. We report on the ultraviolet properties of a sample of early-type (ellipticals+S0s) galaxies inhabiting the Red Sequence. The analysis of their structures, as derived by fitting a Sérsic law to their ultraviolet luminosity profiles, suggests the presence of an underlying disk. This is the hallmark of dissipation processes that still must have a role to play in the evolution of this class of galaxies. Smooth particle hydrodynamic simulations with chemo-photometric implementations able to match the global properties of our targets are used to derive their evolutionary paths through ultraviolet-optical colour magnitude diagrams, providing some fundamental information such as the crossing time through the Green Valley, which depends on their luminosity. The transition from the Blue Cloud to the Red Sequence takes several Gyrs, being about 3-5 Gyr for the brightest galaxies and longer for fainter ones, if occurring. The photometric study of nearby galaxy structures in the ultraviolet is seriously hampered by either the limited field of view of the cameras (e.g., in Hubble Space Telescope) or by the low spatial resolution of the images (e.g., in the Galaxy Evolution Explorer). Current missions equipped with telescopes and cameras sensitive to ultraviolet wavelengths, such as Swift- UVOT and Astrosat-UVIT, provide a relatively large field of view and a better resolution than the Galaxy Evolution Explorer. More powerful ultraviolet instruments (size, resolution and field of view) are obviously bound to yield fundamental advances in the accuracy and depth of the surface photometry and in the characterisation of the galaxy environment.

Evaluation of anemia diagnosis based on elastic light scattering (Conference Presentation)

NASA Astrophysics Data System (ADS)

Tong, Lieshu; Wang, Xinrui; Xie, Dengling; Chen, Xiaoya; Chu, Kaiqin; Dou, Hu; Smith, Zachary J.

2017-03-01

Currently, one-third of humanity is still suffering from anemia. In China the most common forms of anemia are iron deficiency and Thalassemia minor. Differentiating these two is the key to effective treatment. Iron deficiency is caused by malnutrition and can be cured by iron supplementation. Thalassemia is a hereditary disease in which the hemoglobin β chain is lowered or absent. Iron therapy is not effective, and there is evidence that iron therapy may be harmful to patients with Thalassemia. Both anemias can be diagnosed using red blood cell morphology: Iron deficiency presents a smaller mean cell volume compared to normal cells, but with a wide distribution; Thalassemia, meanwhile, presents a very small cell size and tight particle size distribution. Several researchers have proposed diagnostic indices based on red cell morphology to differentiate these two diseases. However, these indices lack sensitivity and specificity and are constructed without statistical rigor. Using multivariate methods we demonstrate a new classification method based on red cell morphology that diagnoses anemia in a Chinese population with enough accuracy for its use as a screening method. We further demonstrate a low cost instrument that precisely measures red cell morphology using elastic light scattering. This instrument is combined with an automated analysis program that processes scattering data to report red cell morphology without the need for user intervention. Despite using consumer-grade components, when comparing our experimental results with gold-standard measurements, the device can still achieve the high precision required for sensing clinically significant changes in red cell morphology.

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.

Tight Loops Close-Up [video

NASA Image and Video Library

2014-05-19

NASA's Solar Dynamics Observatory (SDO) zoomed in almost to its maximum level to watch tight, bright loops and much longer, softer loops shift and sway above an active region on the sun, while a darker blob of plasma in their midst was pulled about every which way (May 13-14, 2014). The video clip covers just over a day beginning at 14:19 UT on May 13. The frames were taken in the 171-angstroms wavelength of extreme ultraviolet light, but colorized red, instead of its usual bronze tone. This type of dynamic activity continues almost non-stop on the sun as opposing magnetic forces tangle with each other. Credit: NASA/Solar Dynamics Observatory NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

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.

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.

Decoupling of epitaxial graphene via gold intercalation probed by dispersive Raman spectroscopy

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

Pillai, P. B., E-mail: p.pillai@sheffield.ac.uk, E-mail: m.desouza@sheffield.ac.uk; DeSouza, M., E-mail: p.pillai@sheffield.ac.uk, E-mail: m.desouza@sheffield.ac.uk; Narula, R.

Signatures of a superlattice structure composed of a quasi periodic arrangement of atomic gold clusters below an epitaxied graphene (EG) layer are examined using dispersive Raman spectroscopy. The gold-graphene system exhibits a laser excitation energy dependant red shift of the 2D mode as compared to pristine epitaxial graphene. The phonon dispersions in both the systems are mapped using the experimentally observed Raman signatures and a third-nearest neighbour tight binding electronic band structure model. Our results reveal that the observed excitation dependent Raman red shift in gold EG primarily arise from the modifications of the phonon dispersion in gold-graphene and showsmore » that the extent of decoupling of graphene from the underlying SiC substrate can be monitored from the dispersive nature of the Raman 2D modes. The intercalated gold atoms restore the phonon band structure of epitaxial graphene towards free standing graphene.« less

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

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

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.

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.

Nonspecific Adherence by Actinobacillus actinomycetemcomitans Requires Genes Widespread in Bacteria and Archaea

PubMed Central

Kachlany, Scott C.; Planet, Paul J.; Bhattacharjee, Mrinal K.; Kollia, Evyenia; DeSalle, Rob; Fine, Daniel H.; Figurski, David H.

2000-01-01

The gram-negative coccobacillus, Actinobacillus actinomycetemcomitans, is the putative agent for localized juvenile periodontitis, a particularly destructive form of periodontal disease in adolescents. This bacterium has also been isolated from a variety of other infections, notably endocarditis. Fresh clinical isolates of A. actinomycetemcomitans form tenacious biofilms, a property likely to be critical for colonization of teeth and other surfaces. Here we report the identification of a locus of seven genes required for nonspecific adherence of A. actinomycetemcomitans to surfaces. The recently developed transposon IS903φkan was used to isolate mutants of the rough clinical isolate CU1000 that are defective in tight adherence to surfaces (Tad−). Unlike wild-type cells, Tad− mutant cells adhere poorly to surfaces, fail to form large autoaggregates, and lack long, bundled fibrils. Nucleotide sequencing and genetic complementation analysis revealed a 6.7-kb region of the genome with seven adjacent genes (tadABCDEFG) required for tight adherence. The predicted TadA polypeptide is similar to VirB11, an ATPase involved in macromolecular transport. The predicted amino acid sequences of the other Tad polypeptides indicate membrane localization but no obvious functions. We suggest that the tad genes are involved in secretion of factors required for tight adherence of A. actinomycetemcomitans. Remarkably, complete and highly conserved tad gene clusters are present in the genomes of the bubonic plague bacillus Yersinia pestis and the human and animal pathogen Pasteurella multocida. Partial tad loci also occur in strikingly diverse Bacteria and Archaea. Our results show that the tad genes are required for tight adherence of A. actinomycetemcomitans to surfaces and are therefore likely to be essential for colonization and pathogenesis. The occurrence of similar genes in a wide array of microorganisms indicates that they have important functions. We propose that tad-like genes have a significant role in microbial colonization. PMID:11029439

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.

Prediction and analysis of beta-turns in proteins by support vector machine.

PubMed

Pham, Tho Hoan; Satou, Kenji; Ho, Tu Bao

2003-01-01

Tight turn has long been recognized as one of the three important features of proteins after the alpha-helix and beta-sheet. Tight turns play an important role in globular proteins from both the structural and functional points of view. More than 90% tight turns are beta-turns. Analysis and prediction of beta-turns in particular and tight turns in general are very useful for the design of new molecules such as drugs, pesticides, and antigens. In this paper, we introduce a support vector machine (SVM) approach to prediction and analysis of beta-turns. We have investigated two aspects of applying SVM to the prediction and analysis of beta-turns. First, we developed a new SVM method, called BTSVM, which predicts beta-turns of a protein from its sequence. The prediction results on the dataset of 426 non-homologous protein chains by sevenfold cross-validation technique showed that our method is superior to the other previous methods. Second, we analyzed how amino acid positions support (or prevent) the formation of beta-turns based on the "multivariable" classification model of a linear SVM. This model is more general than the other ones of previous statistical methods. Our analysis results are more comprehensive and easier to use than previously published analysis results.

A Simplified Baseband Prefilter Model with Adaptive Kalman Filter for Ultra-Tight COMPASS/INS Integration

PubMed Central

Luo, Yong; Wu, Wenqi; Babu, Ravindra; Tang, Kanghua; Luo, Bing

2012-01-01

COMPASS is an indigenously developed Chinese global navigation satellite system and will share many features in common with GPS (Global Positioning System). Since the ultra-tight GPS/INS (Inertial Navigation System) integration shows its advantage over independent GPS receivers in many scenarios, the federated ultra-tight COMPASS/INS integration has been investigated in this paper, particularly, by proposing a simplified prefilter model. Compared with a traditional prefilter model, the state space of this simplified system contains only carrier phase, carrier frequency and carrier frequency rate tracking errors. A two-quadrant arctangent discriminator output is used as a measurement. Since the code tracking error related parameters were excluded from the state space of traditional prefilter models, the code/carrier divergence would destroy the carrier tracking process, and therefore an adaptive Kalman filter algorithm tuning process noise covariance matrix based on state correction sequence was incorporated to compensate for the divergence. The federated ultra-tight COMPASS/INS integration was implemented with a hardware COMPASS intermediate frequency (IF), and INS's accelerometers and gyroscopes signal sampling system. Field and simulation test results showed almost similar tracking and navigation performances for both the traditional prefilter model and the proposed system; however, the latter largely decreased the computational load. PMID:23012564

An Adaptive Low-Cost INS/GNSS Tightly-Coupled Integration Architecture Based on Redundant Measurement Noise Covariance Estimation.

PubMed

Li, Zheng; Zhang, Hai; Zhou, Qifan; Che, Huan

2017-09-05

The main objective of the introduced study is to design an adaptive Inertial Navigation System/Global Navigation Satellite System (INS/GNSS) tightly-coupled integration system that can provide more reliable navigation solutions by making full use of an adaptive Kalman filter (AKF) and satellite selection algorithm. To achieve this goal, we develop a novel redundant measurement noise covariance estimation (RMNCE) theorem, which adaptively estimates measurement noise properties by analyzing the difference sequences of system measurements. The proposed RMNCE approach is then applied to design both a modified weighted satellite selection algorithm and a type of adaptive unscented Kalman filter (UKF) to improve the performance of the tightly-coupled integration system. In addition, an adaptive measurement noise covariance expanding algorithm is developed to mitigate outliers when facing heavy multipath and other harsh situations. Both semi-physical simulation and field experiments were conducted to evaluate the performance of the proposed architecture and were compared with state-of-the-art algorithms. The results validate that the RMNCE provides a significant improvement in the measurement noise covariance estimation and the proposed architecture can improve the accuracy and reliability of the INS/GNSS tightly-coupled systems. The proposed architecture can effectively limit positioning errors under conditions of poor GNSS measurement quality and outperforms all the compared schemes.

An Adaptive Low-Cost INS/GNSS Tightly-Coupled Integration Architecture Based on Redundant Measurement Noise Covariance Estimation

PubMed Central

Li, Zheng; Zhang, Hai; Zhou, Qifan; Che, Huan

2017-01-01

The main objective of the introduced study is to design an adaptive Inertial Navigation System/Global Navigation Satellite System (INS/GNSS) tightly-coupled integration system that can provide more reliable navigation solutions by making full use of an adaptive Kalman filter (AKF) and satellite selection algorithm. To achieve this goal, we develop a novel redundant measurement noise covariance estimation (RMNCE) theorem, which adaptively estimates measurement noise properties by analyzing the difference sequences of system measurements. The proposed RMNCE approach is then applied to design both a modified weighted satellite selection algorithm and a type of adaptive unscented Kalman filter (UKF) to improve the performance of the tightly-coupled integration system. In addition, an adaptive measurement noise covariance expanding algorithm is developed to mitigate outliers when facing heavy multipath and other harsh situations. Both semi-physical simulation and field experiments were conducted to evaluate the performance of the proposed architecture and were compared with state-of-the-art algorithms. The results validate that the RMNCE provides a significant improvement in the measurement noise covariance estimation and the proposed architecture can improve the accuracy and reliability of the INS/GNSS tightly-coupled systems. The proposed architecture can effectively limit positioning errors under conditions of poor GNSS measurement quality and outperforms all the compared schemes. PMID:28872629

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.

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.

What Is The Color Of The Milky Way?

NASA Astrophysics Data System (ADS)

Licquia, Timothy; Newman, J. A.

2012-01-01

For most galaxies with known redshift, the properties we can measure best are their color and luminosity, making these quantities vital for classifying galaxies from the local universe to high z. However, it is difficult to determine these same properties for the Milky Way, the galaxy we can study in the most detail, due to our location within it. Here, we employ a new approach which is immune to the effects of interstellar reddening. Using new infrared measurements of the Milky Way's star-formation rate and dynamical measurements of its stellar mass (along with their attendant uncertainties), we identify samples of galaxies in Sloan Digital Sky Survey data with matching properties, and evaluate the distribution of colors and luminosities of these analogs. Essentially, we make the Copernican assumption that the Milky Way is not unusual for a galaxy of its mass and star formation rate. This procedure tightly constrains the possible photometric properties of the Milky Way; we present results for both ugriz colors and absolute magnitudes, and explore the impact of potential systematic errors. We also present a gallery of images of galaxies whose properties should be similar to those of the Milky Way. Our results show that the Milky Way must be amongst the brightest, reddest star-forming spiral galaxies, with an overall color which is likely only slightly bluer than the bluest red sequence galaxies.

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.

Hydro-mechanical properties of the Red Salt Clay (T4) - Relevancy of the minimum stress criterion for barrier integrity

NASA Astrophysics Data System (ADS)

Minkley, W.; Popp, T.; Salzer, K.; Gruner, M.; Böttge, V.

The so-called Red Salt Clay (T4) is deposited as clay-rich clastic sediment at the base of the Aller-series forming a persistent lateral layer of up to 20 m thickness above the lower Zechstein-series. The clay layers may act as a protective shield in the hanging wall of gas storages or underground repositories in salt formations, thus resulting in a multi-barrier system. As a proof of its reliability comprehensive hydro-mechanical investigations were performed on clay samples recovered at different sites in Germany. Most important, rock tightness against various fluids was confirmed in the lab and field-scale. Remarkably, only if the fluid pressure equalises the acting minimal stress (i.e. violence of the “minimum stress criterion”) a significant increase of permeability is observed (“pathway dilatation”) but no macro-frac. However, the material properties from different locations showed a significant variability according to different burial depths. Thus the Red Salt Clay may act as natural analogue, representing the material variability of various indurated clays. In addition, the existing knowledge gained from practical mining activities can be used to evaluate extreme in situ loading conditions.

Mapping and monitoring Mt. Graham Red Squirrel habitat with GIS and thematic mapper imagery

USGS Publications Warehouse

Hatten, James R.; Koprowski, John L.; Sanderson, H. Reed; Koprowski, John L.

2009-01-01

To estimate the Mt. Graham red squirrel (MGRS) population, personnel visit a proportion of middens each year to determine their occupancy (Snow in this vol.). The method results in very tight confidence intervals (high precision), but the accuracy of the population estimate is dependent upon knowing where all the middens are located. I hypothesized that there might be areas outside the survey boundary that contained Mt. Graham red squirrel middens, but the ruggedness of the Pinaleno Mountains made mountain-wide surveys difficult. Therefore, I started exploring development of a spatially explicit (geographic information system [GIS]-based) habitat model in 1998 that could identify MGRS habitat remotely with satellite imagery and a GIS. A GIS-based model would also allow us to assess changes in MGRS habitat between two time periods because Landsat passes over the same location every 16 days, imaging the earth in 185 km swaths (Aronoff 1989). Specifically, the objectives of this analysis were to (1) develop a pattern recognition model for MGRS habitat, (2) map potential (predicted/modeled) MGRS habitat, (3) identify changes in potential MGRS habitat between 1993 and 2003, and (4) evaluate the current location of the MGRS survey boundary.

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.

Disordered eating and eating disorders in aquatic sports.

PubMed

Melin, Anna; Torstveit, Monica Klungland; Burke, Louise; Marks, Saul; Sundgot-Borgen, Jorunn

2014-08-01

Disordered eating behavior (DE) and eating disorders (EDs) are of great concern because of their associations with physical and mental health risks and, in the case of athletes, impaired performance. The syndrome originally known as the Female Athlete Triad, which focused on the interaction of energy availability, reproductive function, and bone health in female athletes, has recently been expanded to recognize that Relative Energy Deficiency in Sport (RED-S) has a broader range of negative effects on body systems with functional impairments in both male and female athletes. Athletes in leanness-demanding sports have an increased risk for RED-S and for developing EDs/DE. Special risk factors in aquatic sports related to weight and body composition management include the wearing of skimpy and tight-fitting bathing suits, and in the case of diving and synchronized swimming, the involvement of subjective judgments of performance. The reported prevalence of DE and EDs in athletic populations, including athletes from aquatic sports, ranges from 18 to 45% in female athletes and from 0 to 28% in male athletes. To prevent EDs, aquatic athletes should practice healthy eating behavior at all periods of development pathway, and coaches and members of the athletes' health care team should be able to recognize early symptoms indicating risk for energy deficiency, DE, and EDs. Coaches and leaders must accept that DE/EDs can be a problem in aquatic disciplines and that openness regarding this challenge is important.

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

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.

An Adaptive Low-Cost GNSS/MEMS-IMU Tightly-Coupled Integration System with Aiding Measurement in a GNSS Signal-Challenged Environment

PubMed Central

Zhou, Qifan; Zhang, Hai; Li, You; Li, Zheng

2015-01-01

The main aim of this paper is to develop a low-cost GNSS/MEMS-IMU tightly-coupled integration system with aiding information that can provide reliable position solutions when the GNSS signal is challenged such that less than four satellites are visible in a harsh environment. To achieve this goal, we introduce an adaptive tightly-coupled integration system with height and heading aiding (ATCA). This approach adopts a novel redundant measurement noise estimation method for an adaptive Kalman filter application and also augments external measurements in the filter to aid the position solutions, as well as uses different filters to deal with various situations. On the one hand, the adaptive Kalman filter makes use of the redundant measurement system’s difference sequence to estimate and tune noise variance instead of employing a traditional innovation sequence to avoid coupling with the state vector error. On the other hand, this method uses the external height and heading angle as auxiliary references and establishes a model for the measurement equation in the filter. In the meantime, it also changes the effective filter online based on the number of tracked satellites. These measures have increasingly enhanced the position constraints and the system observability, improved the computational efficiency and have led to a good result. Both simulated and practical experiments have been carried out, and the results demonstrate that the proposed method is effective at limiting the system errors when there are less than four visible satellites, providing a satisfactory navigation solution. PMID:26393605

An Adaptive Low-Cost GNSS/MEMS-IMU Tightly-Coupled Integration System with Aiding Measurement in a GNSS Signal-Challenged Environment.

PubMed

Zhou, Qifan; Zhang, Hai; Li, You; Li, Zheng

2015-09-18

The main aim of this paper is to develop a low-cost GNSS/MEMS-IMU tightly-coupled integration system with aiding information that can provide reliable position solutions when the GNSS signal is challenged such that less than four satellites are visible in a harsh environment. To achieve this goal, we introduce an adaptive tightly-coupled integration system with height and heading aiding (ATCA). This approach adopts a novel redundant measurement noise estimation method for an adaptive Kalman filter application and also augments external measurements in the filter to aid the position solutions, as well as uses different filters to deal with various situations. On the one hand, the adaptive Kalman filter makes use of the redundant measurement system's difference sequence to estimate and tune noise variance instead of employing a traditional innovation sequence to avoid coupling with the state vector error. On the other hand, this method uses the external height and heading angle as auxiliary references and establishes a model for the measurement equation in the filter. In the meantime, it also changes the effective filter online based on the number of tracked satellites. These measures have increasingly enhanced the position constraints and the system observability, improved the computational efficiency and have led to a good result. Both simulated and practical experiments have been carried out, and the results demonstrate that the proposed method is effective at limiting the system errors when there are less than four visible satellites, providing a satisfactory navigation solution.

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.

Red Misfits in the Sloan Digital Sky Survey: properties of star-forming red galaxies

NASA Astrophysics Data System (ADS)

Evans, Fraser A.; Parker, Laura C.; Roberts, Ian D.

2018-06-01

We study Red Misfits, a population of red, star-forming galaxies in the local Universe. We classify galaxies based on inclination-corrected optical colours and specific star formation rates derived from the Sloan Digital Sky Survey Data Release 7. Although the majority of blue galaxies are star-forming and most red galaxies exhibit little to no ongoing star formation, a small but significant population of galaxies (˜11 per cent at all stellar masses) are classified as red in colour yet actively star-forming. We explore a number of properties of these galaxies and demonstrate that Red Misfits are not simply dusty or highly inclined blue cloud galaxies or quiescent red galaxies with poorly constrained star formation. The proportion of Red Misfits is nearly independent of environment, and this population exhibits both intermediate morphologies and an enhanced likelihood of hosting an active galactic nucleus. We conclude that Red Misfits are a transition population, gradually quenching on their way to the red sequence and this quenching is dominated by internal processes rather than environmentally driven processes. We discuss the connection between Red Misfits and other transition galaxy populations, namely S0s, red spirals, and green valley galaxies.

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

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.

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.

A Homozygous Mutation in the Tight-Junction Protein JAM3 Causes Hemorrhagic Destruction of the Brain, Subependymal Calcification, and Congenital Cataracts

PubMed Central

Mochida, Ganeshwaran H.; Ganesh, Vijay S.; Felie, Jillian M.; Gleason, Danielle; Hill, R. Sean; Clapham, Katie Rose; Rakiec, Daniel; Tan, Wen-Hann; Akawi, Nadia; Al-Saffar, Muna; Partlow, Jennifer N.; Tinschert, Sigrid; Barkovich, A. James; Ali, Bassam; Al-Gazali, Lihadh; Walsh, Christopher A.

2010-01-01

The tight junction, or zonula occludens, is a specialized cell-cell junction that regulates epithelial and endothelial permeability, and it is an essential component of the blood-brain barrier in the cerebrovascular endothelium. In addition to functioning as a diffusion barrier, tight junctions are also involved in signal transduction. In this study, we identified a homozygous mutation in the tight-junction protein gene JAM3 in a large consanguineous family from the United Arab Emirates. Some members of this family had a rare autosomal-recessive syndrome characterized by severe hemorrhagic destruction of the brain, subependymal calcification, and congenital cataracts. Their clinical presentation overlaps with some reported cases of pseudo-TORCH syndrome as well as with cases involving mutations in occludin, another component of the tight-junction complex. However, massive intracranial hemorrhage distinguishes these patients from others. Homozygosity mapping identified the disease locus in this family on chromosome 11q25 with a maximum multipoint LOD score of 6.15. Sequence analysis of genes in the candidate interval uncovered a mutation in the canonical splice-donor site of intron 5 of JAM3. RT-PCR analysis of a patient lymphoblast cell line confirmed abnormal splicing, leading to a frameshift mutation with early termination. JAM3 is known to be present in vascular endothelium, although its roles in cerebral vasculature have not been implicated. Our results suggest that JAM3 is essential for maintaining the integrity of the cerebrovascular endothelium as well as for normal lens development in humans. PMID:21109224

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....

Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants

DOE PAGES

Liang, Yan; Richardson, Sarah; Yan, Jingwei; ...

2017-01-17

Tight control and multifactorial regulation of gene expression are important challenges in genetic engineering and are critical for the development of regulatory circuits. In meeting these challenges we will facilitate transgene expression regulation and support the fine-tuning of metabolic pathways to avoid the accumulation of undesired intermediates. By employing the endoribonuclease Csy4 and its recognition sequence from Pseudomonas aeruginosa and manipulating 5'UTR of mRNA, we developed a two-component expression–repression system to tightly control synthesis of transgene products. We demonstrated that this regulatory device was functional in monocotyledonous and dicotyledonous plant species, and showed that it can be used to repressmore » transgene expression by >400-fold and to synchronize transgene repression. In addition to tissue-specific transgene repression, this system offers stimuli-dependent expression control. Here, we identified 54 orthologous systems from various bacteria, using a bioinformatics approach and then validated in planta the activity for a few of those systems, demonstrating the potential diversity of such a two-component repressor system.« less

Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants

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

Liang, Yan; Richardson, Sarah; Yan, Jingwei

Tight control and multifactorial regulation of gene expression are important challenges in genetic engineering and are critical for the development of regulatory circuits. In meeting these challenges we will facilitate transgene expression regulation and support the fine-tuning of metabolic pathways to avoid the accumulation of undesired intermediates. By employing the endoribonuclease Csy4 and its recognition sequence from Pseudomonas aeruginosa and manipulating 5'UTR of mRNA, we developed a two-component expression–repression system to tightly control synthesis of transgene products. We demonstrated that this regulatory device was functional in monocotyledonous and dicotyledonous plant species, and showed that it can be used to repressmore » transgene expression by >400-fold and to synchronize transgene repression. In addition to tissue-specific transgene repression, this system offers stimuli-dependent expression control. Here, we identified 54 orthologous systems from various bacteria, using a bioinformatics approach and then validated in planta the activity for a few of those systems, demonstrating the potential diversity of such a two-component repressor system.« 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

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants.

PubMed

Li, Shu-Fen; Su, Ting; Cheng, Guang-Qian; Wang, Bing-Xiao; Li, Xu; Deng, Chuan-Liang; Gao, Wu-Jun

2017-10-24

Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation.

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.

Identification of a new retrotransposable element in loblolly pine

Treesearch

M.N. Islam-Faridi; A.M. Morse; K.E. Smith; J.M. Davis; S. Garcia; H.V. Amerson; M.A. Majid; T.L. Kubisiak; C.D. Nelson

2005-01-01

We initiated a project to locate the genomic position of fusiform rust resistance gene 1 (Fr1) in loblolly pine using fluorescent in situ hybridization (FISH). Four random amplified polymorphic DNA (RAPD) markers previously found to be tightly linked to Fr1 were cloned and sequenced, providing a total coverage of about 2 Kb. In order to obtain discernible signal of...

Phylogenetic analysis of Bacillus subtilis strains applicable to natto (fermented soybean) production.

PubMed

Kubo, Yuji; Rooney, Alejandro P; Tsukakoshi, Yoshiki; Nakagawa, Rikio; Hasegawa, Hiromasa; Kimura, Keitarou

2011-09-01

Spore-forming Bacillus strains that produce extracellular poly-γ-glutamic acid were screened for their application to natto (fermented soybean food) fermentation. Among the 424 strains, including Bacillus subtilis and B. amyloliquefaciens, which we isolated from rice straw, 59 were capable of fermenting natto. Biotin auxotrophism was tightly linked to natto fermentation. A multilocus nucleotide sequence of six genes (rpoB, purH, gyrA, groEL, polC, and 16S rRNA) was used for phylogenetic analysis, and amplified fragment length polymorphism (AFLP) analysis was also conducted on the natto-fermenting strains. The ability to ferment natto was inferred from the two principal components of the AFLP banding pattern, and natto-fermenting strains formed a tight cluster within the B. subtilis subsp. subtilis group.

Phylogenetic Analysis of Bacillus subtilis Strains Applicable to Natto (Fermented Soybean) Production ▿

PubMed Central

Kubo, Yuji; Rooney, Alejandro P.; Tsukakoshi, Yoshiki; Nakagawa, Rikio; Hasegawa, Hiromasa; Kimura, Keitarou

2011-01-01

Spore-forming Bacillus strains that produce extracellular poly-γ-glutamic acid were screened for their application to natto (fermented soybean food) fermentation. Among the 424 strains, including Bacillus subtilis and B. amyloliquefaciens, which we isolated from rice straw, 59 were capable of fermenting natto. Biotin auxotrophism was tightly linked to natto fermentation. A multilocus nucleotide sequence of six genes (rpoB, purH, gyrA, groEL, polC, and 16S rRNA) was used for phylogenetic analysis, and amplified fragment length polymorphism (AFLP) analysis was also conducted on the natto-fermenting strains. The ability to ferment natto was inferred from the two principal components of the AFLP banding pattern, and natto-fermenting strains formed a tight cluster within the B. subtilis subsp. subtilis group. PMID:21764950

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...

Short, multiple-stranded β-hairpin peptides have antimicrobial potency with high selectivity and salt resistance.

PubMed

Chou, Shuli; Shao, Changxuan; Wang, Jiajun; Shan, Anshan; Xu, Lin; Dong, Na; Li, Zhongyu

2016-01-01

The β-hairpin structure has been proposed to exhibit potent antimicrobial properties with low cytotoxicity, thus, multiple β-hairpin structures have been proved to be highly stable in structures containing tightly packed hydrophobic cores. The aim of this study was to develop peptide-based synthetic strategies for generating short, but effective AMPs as inexpensive antimicrobial agents. Multiple-stranded β-hairpin peptides with the same β-hairpin unit, (WRXxRW)n where n=1, 2, 3, or 4 and Xx represent the turn sequence, were synthesized, and their potential as antimicrobial agents was evaluated. Owning to the tightly packed hydrophobic core and paired Trp of this multiple-stranded β-hairpin structure, all the 12-residues peptides exhibited high cell selectivity towards bacterial cells over human red blood cells (hRBCs), and the peptide W2 exhibited stronger antimicrobial activities with the MIC values of 2-8μM against various tested bacteria. Not only that, but W2 also showed obvious synergy with streptomycin and chloramphenicol against Escherichia coli, and displayed synergy with ciprofloxacin against Staphylococcus aureus with the FICI values ⩽0.5. Fluorescence spectroscopy and electron microscopy analyses indicated that W2 kills microbial cells by permeabilizing the cell membrane and damaging membrane integrity. Collectively, based on the multiple β-hairpin peptides, the ability to develop libraries of short and effective peptides will be a powerful approach to the discovery of novel antimicrobial agents. We successfully screened a peptide W2 ((WRPGRW)2) from a series of multiple-stranded β-hairpin antimicrobial peptides based on the "S-shaped" motif that induced the formation of a globular structure, and Trp zipper was used to replace the disulfide bonds to reduce the cost of production. This novel structure applied to AMPs improved cell selectivity and salt stability. The findings of this study will promote the development of peptide-based antimicrobial biomaterials. Further exploration of these AMPs will allow for diverse biotechnological and clinical applications such as biomedical coating, food storaging, and animal feeding. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Effects of the Laramide Structures on the Regional Distribution of Tight-Gas Sandstone in the Upper Mesaverde Group, Uinta Basin, Utah

NASA Astrophysics Data System (ADS)

Sitaula, R. P.; Aschoff, J.

2013-12-01

Regional-scale sequence stratigraphic correlation, well log analysis, syntectonic unconformity mapping, isopach maps, and depositional environment maps of the upper Mesaverde Group (UMG) in Uinta basin, Utah suggest higher accommodation in northeastern part (Natural Buttes area) and local development of lacustrine facies due to increased subsidence caused by uplift of San Rafael Swell (SRS) in southern and Uinta Uplift in northern parts. Recently discovered lacustrine facies in Natural Buttes area are completely different than the dominant fluvial facies in outcrops along Book Cliffs and could have implications for significant amount of tight-gas sand production from this area. Data used for sequence stratigraphic correlation, isopach maps and depositional environmental maps include > 100 well logs, 20 stratigraphic profiles, 35 sandstone thin sections and 10 outcrop-based gamma ray profiles. Seven 4th order depositional sequences (~0.5 my duration) are identified and correlated within UMG. Correlation was constructed using a combination of fluvial facies and stacking patterns in outcrops, chert-pebble conglomerates and tidally influenced strata. These surfaces were extrapolated into subsurface by matching GR profiles. GR well logs and core log of Natural Buttes area show intervals of coarsening upward patterns suggesting possible lacustrine intervals that might contain high TOC. Locally, younger sequences are completely truncated across SRS whereas older sequences are truncated and thinned toward SRS. The cycles of truncation and thinning represent phases of SRS uplift. Thinning possibly related with the Uinta Uplift is also observed in northwestern part. Paleocurrents are consistent with interpretation of periodic segmentation and deflection of sedimentation. Regional paleocurrents are generally E-NE-directed in Sequences 1-4, and N-directed in Sequences 5-7. From isopach maps and paleocurrent direction it can be interpreted that uplift of SRS changed route of sediment supply from west to southwest. Locally, paleocurrents are highly variable near SRS further suggesting UMG basin-fill was partitioned by uplift of SRS. Sandstone composition analysis also suggests the uplift of SRS causing the variation of source rocks in upper sequences than the lower sequences. In conclusion, we suggest that Uinta basin was episodically partitioned during the deposition of UMG due to uplift of Laramide structures in the basin and accommodation was localized in northeastern part. Understanding of structural controls on accommodation, sedimentation patterns and depositional environments will aid prediction of the best-producing gas reservoirs.

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.

The EspF N-Terminal of Enterohemorrhagic Escherichia coli O157:H7 EDL933w Imparts Stronger Toxicity Effects on HT-29 Cells than the C-Terminal

PubMed Central

Wang, Xiangyu; Du, Yanli; Hua, Ying; Fu, Muqing; Niu, Cong; Zhang, Bao; Zhao, Wei; Zhang, Qiwei; Wan, Chengsong

2017-01-01

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 EspF is an important multifunctional protein that destroys the tight junctions of intestinal epithelial cells and promotes host cell apoptosis. However, its molecular mechanism remains elusive. We knocked out the espF sequence (747 bp, ΔespF), N-terminal sequence (219 bp, ΔespFN), and C-terminal sequence (528 bp, ΔespFC) separately using the pKD46-mediated λ Red homologous recombination system. Then, we built the corresponding complementation strains, namely, ΔespF/pespF, ΔespFN/pespFN, and ΔespFC/pespFC by overlap PCR, which were used in infecting HT-29 cells and BALB/C mice. The level of reactive oxygen species, cell apoptosis, mitochondrial trans-membrane potential, inflammatory factors, transepithelial electrical resistance (TER), and animal mortality were evaluated by DCFH-DA, double staining of Annexin V-FITC/PI, JC-1 staining, ELISA kit, and a mouse assay. The wild-type (WT), ΔespF, ΔespF/pespF, ΔespFC, ΔespFC/pespFC, ΔespFN, and ΔespFN/pespFN groups exhibited apoptotic rates of 68.3, 27.9, 64.9, 65.7, 73.4, 41.3, and 35.3% respectively, and mean TNF-α expression levels of 428 pg/mL, 342, 466, 446, 381, 383, and 374 pg/mL, respectively. In addition, the apoptotic rates and TNF-α levels of the WT, ΔespF/pespF, and ΔespFC were significantly higher than that of ΔespF, ΔespFN, ΔespFC/pespFC, and ΔespFN/pespFN group (p < 0.05). The N-terminal of EspF resulted in an increase in the number of apoptotic cells, TNF-α secretion, ROS generation, mitochondria apoptosis, and pathogenicity in BalB/c mice. In conclusion, the N-terminal domain of the Enterohemorrhagic E. coli O157:H7 EspF more strongly promotes apoptosis and inflammation than the C-terminal domain. PMID:28983470

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.

Novel silicon microchannels device for use in red blood cell deformability studies

NASA Astrophysics Data System (ADS)

Zheng, Xiao-Lin; Liao, Yan-Jian; Zhang, Wen-Xian

2001-10-01

Currently, a number of techniques are used to access cell deformability. We study a novel silicon microchannels device for use in red blood cell deformability. The channels are produced in silicon substrate using microengineering technology. The microgrooves formed in the surface of a single-crystal silicon substrate. They were converted to channels by tightly covering them with an optical flat glass plate. An array of flow channels (number 950 in parallel) have typical dimensions of 5 micrometers width X 5.5 Xm depth, and 30 micrometers length. There the RBC's are forced to pass through channels. Thus, the microchannels are used to simulate human blood capillaries. It provides a specific measurement of individual cell in terms of both flow velocity profile and an index of cell volume while the cell flow through the channels. It dominates the complex cellular flow behavior, such as, the viscosity of whole blood is a nonlinear function of shear rate, index of filtration, etc.

Binding of various ovotransferrin fragments to chick-embryo red cells.

PubMed Central

Oratore, A; D'Andrea, G; Moreton, K; Williams, J

1989-01-01

1. The ability of N- and C-terminal half-molecule fragments of hen ovotransferrin to interact with chick red blood cells (CERBC) has been studied under conditions that allow binding of the transferrin to transferrin receptors to take place, but not the delivery of iron to the cell. Two kinds of half-molecule fragments were used: (a) those which can associate with one another to give a dimer resembling native transferrin and (b) those which cannot associate in this way because they lack a few amino acid residues from their C-terminal ends. 2. Neither N nor C half-molecules alone can bind to the CERBC, but, when both are present, tight binding occurs. 3. Whether or not the half-molecules can associate with one another makes little difference to receptor binding. 4. Given that one of the half-molecules is iron-saturated, the presence or absence of iron in the contralateral half-molecule again makes little difference to receptor binding. PMID:2920021

Phytochrome B and REVEILLE1/2-mediated signalling controls seed dormancy and germination in Arabidopsis.

PubMed

Jiang, Zhimin; Xu, Gang; Jing, Yanjun; Tang, Weijiang; Lin, Rongcheng

2016-08-10

Seeds maintain a dormant state to withstand adverse conditions and germinate when conditions become favourable to give rise to a new generation of flowering plants. Seed dormancy and germination are tightly controlled by internal and external signals. Although phytochrome photoreceptors are proposed to regulate primary seed dormancy, the underlying molecular mechanism remains elusive. Here we show that the REVEILLE1 (RVE1) and RVE2 transcription factors promote primary seed dormancy and repress red/far-red-light-reversible germination downstream of phytochrome B (phyB) in Arabidopsis thaliana. RVE1 and RVE2 expression is downregulated after imbibition and by phyB. RVE1 directly binds to the promoter of GIBBERELLIN 3-OXIDASE 2, inhibits its transcription and thus suppresses the biosynthesis of bioactive gibberellins. In addition, DELAY OF GERMINATION 1 also acts downstream of phyB. This study identifies a signalling pathway that integrates environmental light input with internal factors to control both seed dormancy and germination.

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.

HUBBLE SEES A VAST 'CITY' OF STARS

NASA Technical Reports Server (NTRS)

2002-01-01

In these pictures, a 'city' of a million stars glitters like a New York City skyline. The images capture the globular cluster 47 Tucanae, located 15,000 light-years from Earth in the southern constellation Tucana. Using NASA's Hubble Space Telescope, astronomers went hunting in this large city for planetary companions: bloated gaseous planets that snuggle close to their parent stars, completing an orbit in a quick three to five days. To their surprise, they found none. This finding suggests that the cluster's environment is too hostile for breeding planets or that it lacks the necessary elements for making them. The picture at left, taken by a terrestrial telescope, shows most of the cluster, a tightly packed group of middle-aged stars held together by mutual gravitational attraction. The box near the center represents the Hubble telescope's view. The image at right shows the Hubble telescope's close-up look at a swarm of 35,000 stars near the cluster's central region. The stars are tightly packed together: They're much closer together than our Sun and its closest stars. The picture, taken by the Wide Field and Planetary Camera 2, depicts the stars' natural colors and tells scientists about their composition and age. For example, the red stars denote bright red giants nearing the end of their lives; the more common yellow stars are similar to our middle-aged Sun. Most of the stars in the cluster are believed to have formed about 10 billion years ago. The bright, blue stars -- thought to be remnants of stellar collisions and mergers -- provide a few rejuvenated, energetic stars in an otherwise old system. The Hubble picture was taken in July 1999. Credits for Hubble image: NASA and Ron Gilliland (Space Telescope Science Institute) Credits for ground-based image: David Malin, c Anglo-Australian Observatory

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.

An overview on genome organization of marine organisms.

PubMed

Costantini, Maria

2015-12-01

In this review we will concentrate on some general genome features of marine organisms and their evolution, ranging from vertebrate to invertebrates until unicellular organisms. Before genome sequencing, the ultracentrifugation in CsCl led to high resolution of mammalian DNA (without seeing at the sequence). The analytical profile of human DNA showed that the vertebrate genome is a mosaic of isochores, typically megabase-size DNA segments that belong in a small number of families characterized by different GC levels. The recent availability of a number of fully sequenced genomes allowed mapping very precisely the isochores, based on DNA sequences. Since isochores are tightly linked to biological properties such as gene density, replication timing and recombination, the new level of detail provided by the isochore map helped the understanding of genome structure, function and evolution. This led the current level of knowledge and to further insights. Copyright © 2015. Published by Elsevier B.V.

Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing

PubMed Central

Cheng, Yanfen; Wang, Ying; Li, Yuanfei; Zhang, Yipeng; Liu, Tianyi; Wang, Yu; Sharpton, Thomas J.; Zhu, Weiyun

2017-01-01

The aim of this study was to improve the utilization of rice straw as forage in ruminants by investigating the degradation pattern of rice straw in the dairy cow rumen. Ground up rice straw was incubated in situ in the rumens of three Holstein cows over a period of 72 h. The rumen fluid at 0 h and the rice straw at 0.5, 1, 2, 4, 6, 12, 24, 48, and 72 h were collected for analysis of the bacterial community and the degradation of the rice straw. The bacterial community and the carbohydrate-active enzymes in the rumen fluid were analyzed by metagenomics. The diversity of bacteria loosely and tightly attached to the rice straw was investigated by scanning electron microscopy and Miseq sequencing of 16S rRNA genes. The predominant genus in the rumen fluid was Prevotella, followed by Bacteroides, Butyrivibrio, unclassified Desulfobulbaceae, Desulfovibrio, and unclassified Sphingobacteriaceae. The main enzymes were members of the glycosyl hydrolase family, divided into four categories (cellulases, hemicellulases, debranching enzymes, and oligosaccharide-degrading enzymes), with oligosaccharide-degrading enzymes being the most abundant. No significant degradation of rice straw was observed between 0.5 and 6 h, whereas the rice straw was rapidly degraded between 6 and 24 h. The degradation then gradually slowed between 24 and 72 h. A high proportion of unclassified bacteria were attached to the rice straw and that Prevotella, Ruminococcus, and Butyrivibrio were the predominant classified genera in the loosely and tightly attached fractions. The composition of the loosely attached bacterial community remained consistent throughout the incubation, whereas a significant shift in composition was observed in the tightly attached bacterial community after 6 h of incubation. This shift resulted in a significant reduction in numbers of Bacteroidetes and a significant increase in numbers of Firmicutes. In conclusion, the degradation pattern of rice straw in the dairy cow rumen indicates a strong contribution by tightly attached bacteria, especially after 6 h incubation, but most of these bacteria were not taxonomically characterized. Thus, these bacteria should be further identified and subjected to functional analysis to improve the utilization of crop residues in ruminants. PMID:29163444

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.

Numerical simulation of multi-dimensional NMR response in tight sandstone

NASA Astrophysics Data System (ADS)

Guo, Jiangfeng; Xie, Ranhong; Zou, Youlong; Ding, Yejiao

2016-06-01

Conventional logging methods have limitations in the evaluation of tight sandstone reservoirs. The multi-dimensional nuclear magnetic resonance (NMR) logging method has the advantage that it can simultaneously measure transverse relaxation time (T 2), longitudinal relaxation time (T 1) and diffusion coefficient (D). In this paper, we simulate NMR measurements of tight sandstone with different wettability and saturations by the random walk method and obtain the magnetization decays of Carr-Purcell-Meiboom-Gill pulse sequences with different wait times (TW) and echo spacings (TE) under a magnetic field gradient, resulting in D-T 2-T 1 maps by the multiple echo trains joint inversion method. We also study the effects of wettability, saturation, signal-to-noise ratio (SNR) of data and restricted diffusion on the D-T 2-T 1 maps in tight sandstone. The results show that with decreasing wetting fluid saturation, the surface relaxation rate of the wetting fluid gradually increases and the restricted diffusion phenomenon becomes more and more obvious, which leads to the wetting fluid signal moving along the direction of short relaxation and the direction of the diffusion coefficient decreasing in D-T 2-T 1 maps. Meanwhile, the non-wetting fluid position in D-T 2-T 1 maps does not change with saturation variation. With decreasing SNR, the ability to identify water and oil signals based on NMR maps gradually decreases. The wetting fluid D-T 1 and D-T 2 correlations in NMR diffusion-relaxation maps of tight sandstone are obtained through expanding the wetting fluid restricted diffusion models, and are further applied to recognize the wetting fluid in simulated D-T 2 maps and D-T 1 maps.

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

Up-going Red Water in the Ice at the Bottom of the World: Picture Taking Boxes and Listening Boxes Tell Us How and Why

NASA Astrophysics Data System (ADS)

Carr, C. G.; Pettit, E. C.

2017-12-01

Blood Falls is a place where red water comes out from under ice to the top of the ice and makes a strange red water fall. This ice is part of the big ice at the bottom of the world. The red water only comes out at some times and not every year, but it always comes out at the same place. The red water is important because it has tiny tiny not-animal life that tells us how life could be on other worlds. Knowing about the ice and red water is important because this ice is cold, colder than other ice in other places, and we want to know how water can get through. We didn't know why the red water comes up from under the ice when it does or how. We wanted to understand how the ice breaks and we watched the ice by taking pictures all year to see when the red water comes out. We found out that in the cold part of one year, the red water came out even though the air was not warm enough for water to be water! We think the red water comes out because the red water is blocked under the heavy ice and gets pushed tight. In the cold part of the year, cracks break down from the air into the ice and other cracks break up from under the ice because the red water is so pushed. The cracks from the top and bottom of the ice join, and the red water comes out. We used listening boxes that can feel how the ground moves to understand that the ice is breaking at the bottom and we can see that it breaks at the top of the ice. The red water can stay water and not ice inside the big ice because the red water has tiny pieces of the same stuff that can turn ice into water on the roads. If the ice breaks in the cold time, no water can get in from the top of the ice, so the red water under the ice stays clean from the air water. If the ice breaks in the warm time of year, water could get in from the top of the ice and make the red water under the ice not clean from the air. Since we saw in our pictures that the red water came out in the cold time of year, this means the red water could stay clean from the air. Maybe we can use this to tell us how life on other worlds could stay clean and safe under ice. It can also tell us how water can get through very cold ice.

Performance of the mixed LED light quality on the growth and energy efficiency of Arthrospira platensis.

PubMed

Mao, Ruixin; Guo, Shuangsheng

2018-06-01

The effect of mixed light quality with red, blue, and green LED lamps on the growth of Arthrospira platensis was studied, so as to lay the theoretical and technical basis for establishing a photo-bioreactor lighting system for application in space. Meanwhile, indexes, like morphology, growth rate, photosynthetic pigment compositions, energy efficiency, and main nutritional components, were measured respectively. The results showed that the blue light combined with red light could decrease the tightness of filament, and the effect of green light was opposite. The combination of blue light or green light with red light induced the filaments to get shorter in length. The 8R2B treatment could promote the growth of Arthrospira platensis significantly, and its dry weight reached 1.36 g L -1 , which was 25.93% higher than the control. What's more, 8R2B treatment had the highest contents of carbohydrate and lipid, while 8R2G was rich in protein. 8R0.5G1.5B had the highest efficiency of biomass production, which was 161.53 mg L -1  kW -1  h -1 . Therefore, the combination of red and blue light is more conducive to the growth of Arthrospira platensis, and a higher biomass production and energy utilization efficiency can be achieved simultaneously under the mixed light quality with the ratio of 8R0.5G1.5B.

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.

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.

Nucleotide sequence analysis of the gene encoding the Deinococcus radiodurans surface protein, derived amino acid sequence, and complementary protein chemical studies

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

Peters, J.; Peters, M.; Lottspeich, F.

1987-11-01

The complete nucleotide sequence of the gene encoding the surface (hexagonally packed intermediate (HPI))-layer polypeptide of Deinococcus radiodurans Sark was determined and found to encode a polypeptide of 1036 amino acids. Amino acid sequence analysis of about 30% of the residues revealed that the mature polypeptide consists of at least 978 amino acids. The N terminus was blocked to Edman degradation. The results of proteolytic modification of the HPI layer in situ and M/sub r/ estimations of the HPI polypeptide expressed in Escherichia coli indicated that there is a leader sequence. The N-terminal region contained a very high percentage (29%)more » of threonine and serine, including a cluster of nine consecutive serine or threonine residues, whereas a stretch near the C terminus was extremely rich in aromatic amino acids (29%). The protein contained at least two disulfide bridges, as well as tightly bound reducing sugars and fatty acids.« less

DNA/RNA transverse current sequencing: intrinsic structural noise from neighboring bases

PubMed Central

Alvarez, Jose R.; Skachkov, Dmitry; Massey, Steven E.; Kalitsov, Alan; Velev, Julian P.

2015-01-01

Nanopore DNA sequencing via transverse current has emerged as a promising candidate for third-generation sequencing technology. It produces long read lengths which could alleviate problems with assembly errors inherent in current technologies. However, the high error rates of nanopore sequencing have to be addressed. A very important source of the error is the intrinsic noise in the current arising from carrier dispersion along the chain of the molecule, i.e., from the influence of neighboring bases. In this work we perform calculations of the transverse current within an effective multi-orbital tight-binding model derived from first-principles calculations of the DNA/RNA molecules, to study the effect of this structural noise on the error rates in DNA/RNA sequencing via transverse current in nanopores. We demonstrate that a statistical technique, utilizing not only the currents through the nucleotides but also the correlations in the currents, can in principle reduce the error rate below any desired precision. PMID:26150827

A filtering method to generate high quality short reads using illumina paired-end technology.

PubMed

Eren, A Murat; Vineis, Joseph H; Morrison, Hilary G; Sogin, Mitchell L

2013-01-01

Consensus between independent reads improves the accuracy of genome and transcriptome analyses, however lack of consensus between very similar sequences in metagenomic studies can and often does represent natural variation of biological significance. The common use of machine-assigned quality scores on next generation platforms does not necessarily correlate with accuracy. Here, we describe using the overlap of paired-end, short sequence reads to identify error-prone reads in marker gene analyses and their contribution to spurious OTUs following clustering analysis using QIIME. Our approach can also reduce error in shotgun sequencing data generated from libraries with small, tightly constrained insert sizes. The open-source implementation of this algorithm in Python programming language with user instructions can be obtained from https://github.com/meren/illumina-utils.

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

The ATLAS3D project - XXVII. Cold gas and the colours and ages of early-type galaxies

NASA Astrophysics Data System (ADS)

Young, Lisa M.; Scott, Nicholas; Serra, Paolo; Alatalo, Katherine; Bayet, Estelle; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Bureau, Martin; Crocker, Alison F.; Cappellari, Michele; Davies, Roger L.; Davis, Timothy A.; de Zeeuw, P. T.; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnović, Davor; Kuntschner, Harald; McDermid, Richard M.; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Weijmans, Anne-Marie

2014-11-01

We present a study of the cold gas contents of the ATLAS3D early-type galaxies, in the context of their optical colours, near-ultraviolet colours and Hβ absorption line strengths. Early-type (elliptical and lenticular) galaxies are not as gas poor as previously thought, and at least 40 per cent of local early-type galaxies are now known to contain molecular and/or atomic gas. This cold gas offers the opportunity to study recent galaxy evolution through the processes of cold gas acquisition, consumption (star formation) and removal. Molecular and atomic gas detection rates range from 10 to 34 per cent in red sequence early-type galaxies, depending on how the red sequence is defined, and from 50 to 70 per cent in blue early-type galaxies. Notably, massive red sequence early-type galaxies (stellar masses >5 × 1010 M⊙, derived from dynamical models) are found to have H I masses up to M(H I)/M* ˜ 0.06 and H2 masses up to M(H2)/M* ˜ 0.01. Some 20 per cent of all massive early-type galaxies may have retained atomic and/or molecular gas through their transition to the red sequence. However, kinematic and metallicity signatures of external gas accretion (either from satellite galaxies or the intergalactic medium) are also common, particularly at stellar masses ≤5 × 1010 M⊙, where such signatures are found in ˜50 per cent of H2-rich early-type galaxies. Our data are thus consistent with a scenario in which fast rotator early-type galaxies are quenched former spiral galaxies which have undergone some bulge growth processes, and in addition, some of them also experience cold gas accretion which can initiate a period of modest star formation activity. We discuss implications for the interpretation of colour-magnitude diagrams.

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

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.

PubMed

Dupradeau, François-Yves; Pigache, Adrien; Zaffran, Thomas; Savineau, Corentin; Lelong, Rodolphe; Grivel, Nicolas; Lelong, Dimitri; Rosanski, Wilfried; Cieplak, Piotr

2010-07-28

Deriving atomic charges and building a force field library for a new molecule are key steps when developing a force field required for conducting structural and energy-based analysis using molecular mechanics. Derivation of popular RESP charges for a set of residues is a complex and error prone procedure because it depends on numerous input parameters. To overcome these problems, the R.E.D. Tools (RESP and ESP charge Derive, ) have been developed to perform charge derivation in an automatic and straightforward way. The R.E.D. program handles chemical elements up to bromine in the periodic table. It interfaces different quantum mechanical programs employed for geometry optimization and computing molecular electrostatic potential(s), and performs charge fitting using the RESP program. By defining tight optimization criteria and by controlling the molecular orientation of each optimized geometry, charge values are reproduced at any computer platform with an accuracy of 0.0001 e. The charges can be fitted using multiple conformations, making them suitable for molecular dynamics simulations. R.E.D. allows also for defining charge constraints during multiple molecule charge fitting, which are used to derive charges for molecular fragments. Finally, R.E.D. incorporates charges into a force field library, readily usable in molecular dynamics computer packages. For complex cases, such as a set of homologous molecules belonging to a common family, an entire force field topology database is generated. Currently, the atomic charges and force field libraries have been developed for more than fifty model systems and stored in the RESP ESP charge DDataBase. Selected results related to non-polarizable charge models are presented and discussed.

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.

Genotypic diversity of oscillatoriacean strains belonging to the genera Geitlerinema and Spirulina determined by 16S rDNA restriction analysis.

PubMed

Margheri, Maria C; Piccardi, Raffaella; Ventura, Stefano; Viti, Carlo; Giovannetti, Luciana

2003-05-01

Genotypic diversity of several cyanobacterial strains mostly isolated from marine or brackish waters, belonging to the genera Geitlerinema and Spirulina, was investigated by amplified 16S ribosomal DNA restriction analysis and compared with morphological features and response to salinity. Cluster analysis was performed on amplified 16S rDNA restriction profiles of these strains along with profiles obtained from sequence data of five Spirulina-like strains, including three representatives of the new genus Halospirulina. Our strains with tightly coiled trichomes from hypersaline waters could be assigned to the Halospirulina genus. Among the uncoiled strains, the two strains of hypersaline origin clustered together and were found to be distant from their counterparts of marine and freshwater habitat. Moreover, another cluster, formed by alkali-tolerant strains with tightly coiled trichomes, was well delineated.

‘Eavesdropping’ in wild rough-toothed dolphins (Steno bredanensis)?

PubMed Central

Götz, Thomas; Verfuß, Ursula Katharina; Schnitzler, Hans-Ulrich

2005-01-01

Several authors suggest that dolphins use information obtained by eavesdropping on echoes from sonar signals of conspecifics, but there is little evidence that this strategy is used by dolphins in the wild. Travelling rough-toothed dolphins (Steno bredanensis) either exhibit asynchronous movements or an extremely synchronized swimming behaviour in tight formations, which we expect to facilitate eavesdropping. Therefore, we determined, whether either one or more dolphins were echolocating in subgroups that were travelling with asynchronous and synchronized movements. Since, the number of recording sequences in which more than one animal produced sonar signals was significantly lower during synchronized travel, we conclude that the other members of a subgroup might get information on targets ahead by eavesdropping. Synchronized swimming in tight formations might be an energetic adaptation for travelling in a pelagic dolphin species that facilitates eavesdropping. PMID:17148311

'Eavesdropping' in wild rough-toothed dolphins (Steno bredanensis)?

PubMed

Götz, Thomas; Verfuss, Ursula Katharina; Schnitzler, Hans-Ulrich

2006-03-22

Several authors suggest that dolphins use information obtained by eavesdropping on echoes from sonar signals of conspecifics, but there is little evidence that this strategy is used by dolphins in the wild. Travelling rough-toothed dolphins (Steno bredanensis) either exhibit asynchronous movements or an extremely synchronized swimming behaviour in tight formations, which we expect to facilitate eavesdropping. Therefore, we determined, whether either one or more dolphins were echolocating in subgroups that were travelling with asynchronous and synchronized movements. Since, the number of recording sequences in which more than one animal produced sonar signals was significantly lower during synchronized travel, we conclude that the other members of a subgroup might get information on targets ahead by eavesdropping. Synchronized swimming in tight formations might be an energetic adaptation for travelling in a pelagic dolphin species that facilitates eavesdropping.

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.

Breaking Lander-Waterman’s Coverage Bound

PubMed Central

Nashta-ali, Damoun; Motahari, Seyed Abolfazl; Hosseinkhalaj, Babak

2016-01-01

Lander-Waterman’s coverage bound establishes the total number of reads required to cover the whole genome of size G bases. In fact, their bound is a direct consequence of the well-known solution to the coupon collector’s problem which proves that for such genome, the total number of bases to be sequenced should be O(G ln G). Although the result leads to a tight bound, it is based on a tacit assumption that the set of reads are first collected through a sequencing process and then are processed through a computation process, i.e., there are two different machines: one for sequencing and one for processing. In this paper, we present a significant improvement compared to Lander-Waterman’s result and prove that by combining the sequencing and computing processes, one can re-sequence the whole genome with as low as O(G) sequenced bases in total. Our approach also dramatically reduces the required computational power for the combined process. Simulation results are performed on real genomes with different sequencing error rates. The results support our theory predicting the log G improvement on coverage bound and corresponding reduction in the total number of bases required to be sequenced. PMID:27806058

TRGB Distances to Galaxies in Front of the Virgo Cluster

NASA Astrophysics Data System (ADS)

Karachentsev, Igor D.; Makarova, Lidia N.; Tully, R. Brent; Rizzi, Luca; Shaya, Edward J.

2018-05-01

Tip of the red giant branch distances are acquired from Hubble Space Telescope images for 16 galaxies to the foreground of the Virgo Cluster. The new distances with 5% accuracy, combined with archival measurements, tightly constrain the near-side location of the onset of infall into the Virgo Cluster to be 7.3 ± 0.3 Mpc from the cluster, reaching within 9 Mpc of the Milky Way. The mass within this turnaround radius about the cluster is (8.3 ± 0.9) × 1014 M ⊙. Color–magnitude diagrams are provided for galaxies in this study and there is a brief discussion of their group affiliations.

Support vector machines for prediction and analysis of beta and gamma-turns in proteins.

PubMed

Pham, Tho Hoan; Satou, Kenji; Ho, Tu Bao

2005-04-01

Tight turns have long been recognized as one of the three important features of proteins, together with alpha-helix and beta-sheet. Tight turns play an important role in globular proteins from both the structural and functional points of view. More than 90% tight turns are beta-turns and most of the rest are gamma-turns. Analysis and prediction of beta-turns and gamma-turns is very useful for design of new molecules such as drugs, pesticides, and antigens. In this paper we investigated two aspects of applying support vector machine (SVM), a promising machine learning method for bioinformatics, to prediction and analysis of beta-turns and gamma-turns. First, we developed two SVM-based methods, called BTSVM and GTSVM, which predict beta-turns and gamma-turns in a protein from its sequence. When compared with other methods, BTSVM has a superior performance and GTSVM is competitive. Second, we used SVMs with a linear kernel to estimate the support of amino acids for the formation of beta-turns and gamma-turns depending on their position in a protein. Our analysis results are more comprehensive and easier to use than the previous results in designing turns in proteins.

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.

Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus.

PubMed

Squires, R Burke; Pickett, Brett E; Das, Sajal; Scheuermann, Richard H

2014-12-01

In 2009 a novel pandemic H1N1 influenza virus (H1N1pdm09) emerged as the first official influenza pandemic of the 21st century. Early genomic sequence analysis pointed to the swine origin of the virus. Here we report a novel computational approach to determine the evolutionary trajectory of viral sequences that uses data-driven estimations of nucleotide substitution rates to track the gradual accumulation of observed sequence alterations over time. Phylogenetic analysis and multiple sequence alignments show that sequences belonging to the resulting evolutionary trajectory of the H1N1pdm09 lineage exhibit a gradual accumulation of sequence variations and tight temporal correlations in the topological structure of the phylogenetic trees. These results suggest that our evolutionary trajectory analysis (ETA) can more effectively pinpoint the evolutionary history of viruses, including the host and geographical location traversed by each segment, when compared against either BLAST or traditional phylogenetic analysis alone. Copyright © 2014 Elsevier B.V. All rights reserved.

Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants

PubMed Central

Li, Shu-Fen; Su, Ting; Cheng, Guang-Qian; Wang, Bing-Xiao; Li, Xu; Deng, Chuan-Liang; Gao, Wu-Jun

2017-01-01

Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation. PMID:29064432

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.

Glucocorticoids induce transactivation of tight junction genes occludin and claudin-5 in retinal endothelial cells via a novel cis-element.

PubMed

Felinski, Edward A; Cox, Amy E; Phillips, Brett E; Antonetti, David A

2008-06-01

Tight junctions between vascular endothelial cells help to create the blood-brain and blood-retinal barriers. Breakdown of the retinal tight junction complex is problematic in several disease states including diabetic retinopathy. Glucocorticoids can restore and/or preserve the endothelial barrier to paracellular permeability, although the mechanism remains unclear. We show that glucocorticoid treatment of primary retinal endothelial cells increases content of the tight junction proteins occludin and claudin-5, co-incident with an increase in barrier properties of endothelial monolayers. The glucocorticoid receptor antagonist RU486 reverses both the glucocorticoid-stimulated increase in occludin content and the increase in barrier properties. Transcriptional activity from the human occludin and claudin-5 promoters increases in retinal endothelial cells upon glucocorticoid treatment, and is dependent on the glucocorticoid receptor (GR) as demonstrated by siRNA. Deletion analysis of the occludin promoter reveals a 205bp sequence responsible for the glucocorticoid response. However, this region does not possess a canonical glucocorticoid response element and does not bind to the GR in a chromatin immunoprecipitation (ChIP) assay. Mutational analysis of this region revealed a novel 40bp occludin enhancer element (OEE), containing two highly conserved regions of 10 and 13 base pairs, that is both necessary and sufficient for glucocorticoid-induced gene expression in retinal endothelial cells. These data suggest a novel mechanism for glucocorticoid induction of vascular endothelial barrier properties through increased occludin and claudin-5 gene expression.

GLUCOCORTICOIDS INDUCE TRANSACTIVATION OF TIGHT JUNCTION GENES OCCLUDIN AND CLAUDIN-5 IN RETINAL ENDOTHELIAL CELLS VIA A NOVEL CIS-ELEMENT

PubMed Central

Felinski, Edward A.; Cox, Amy E.; Phillips, Brett E.; Antonetti, David A.

2008-01-01

Tight junctions between vascular endothelial cells help to create the blood-brain and blood-retinal barriers. Breakdown of the retinal tight junction complex is problematic in several disease states including diabetic retinopathy. Glucocorticoids can restore and/or preserve the endothelial barrier to paracellular permeability, although the mechanism remains unclear. We show that glucocorticoid treatment of primary retinal endothelial cells increases content of the tight junction proteins occludin and claudin-5, co-incident with an increase in barrier properties of endothelial monolayers. The glucocorticoid receptor antagonist RU486 reverses both the glucocorticoid-stimulated increase in occludin content and the increase in barrier properties. Transcriptional activity from the human occludin and claudin-5 promoters increases in retinal endothelial cells upon glucocorticoid treatment, and is dependent on the glucocorticoid receptor (GR) as demonstrated by siRNA. Deletion analysis of the occludin promoter reveals a 205 bp sequence responsible for the glucocorticoid response. However, this region does not posses a canonical glucocorticoid response element and does not bind to the GR in a chromatin immunoprecipitation (ChIP) assay. Mutational analysis of this region revealed a novel 40 bp occludin enhancer element (OEE), containing two highly-conserved regions of 10 and 13 base pairs, that is both necessary and sufficient for glucocorticoid-induced gene expression in retinal endothelial cells. These data suggest a novel mechanism for glucocorticoid induction of vascular endothelial barrier properties through increased occludin and claudin-5 gene expression. PMID:18501346

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.

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.

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.

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.

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.

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.

A Cluster of Legionella-Associated Pneumonia Cases in a Population of Military Recruits

DTIC Science & Technology

2007-06-01

this cluster may suggest a previously unrecognized suscep- FIG. 1. Phylogenic analysis of the training center strain (represented by the MCRD consensus...military recruits during population- based surveillance for pneumonia pathogens. Results were confirmed by sequence analysis . Cases cluster tightly...17 April 2007 A Legionella cluster was identified through retrospective PCR analysis of 240 throat swab samples from X-ray-confirmed pneumonia cases

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

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.

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.

Molecular Mechanisms of Enhanced Bacterial Growth on Hexadecane with Red Clay.

PubMed

Jung, Jaejoon; Jang, In-Ae; Ahn, Sungeun; Shin, Bora; Kim, Jisun; Park, Chulwoo; Jee, Seung Cheol; Sung, Jung-Suk; Park, Woojun

2015-11-01

Red clay was previously used to enhance bioremediation of diesel-contaminated soil. It was speculated that the enhanced degradation of diesel was due to increased bacterial growth. In this study, we selected Acinetobacter oleivorans DR1, a soil-borne degrader of diesel and alkanes, as a model bacterium and performed transcriptional analysis using RNA sequencing to investigate the cellular response during hexadecane utilization and the mechanism by which red clay promotes hexadecane degradation. We confirmed that red clay promotes the growth of A. oleivorans DR1 on hexadecane, a major component of diesel, as a sole carbon source. Addition of red clay to hexadecane-utilizing DR1 cells highly upregulated β-oxidation, while genes related to alkane oxidation were highly expressed with and without red clay. Red clay also upregulated genes related to oxidative stress defense, such as superoxide dismutase, catalase, and glutaredoxin genes, suggesting that red clay supports the response of DR1 cells to oxidative stress generated during hexadecane utilization. Increased membrane fluidity in the presence of red clay was confirmed by fatty acid methyl ester analysis at different growth phases, suggesting that enhanced growth on hexadecane could be due to increased uptake of hexadecane coupled with upregulation of downstream metabolism and oxidative stress defense. The monitoring of the bacterial community in soil with red clay for a year revealed that red clay stabilized the community structure.

Transcriptome sequence analysis of an ornamental plant, Ananas comosus var. bracteatus, revealed the potential unigenes involved in terpenoid and phenylpropanoid biosynthesis.

PubMed

Ma, Jun; Kanakala, S; He, Yehua; Zhang, Junli; Zhong, Xiaolan

2015-01-01

Ananas comosus var. bracteatus (Red Pineapple) is an important ornamental plant for its colorful leaves and decorative red fruits. Because of its complex genome, it is difficult to understand the molecular mechanisms involved in the growth and development. Thus high-throughput transcriptome sequencing of Ananas comosus var. bracteatus is necessary to generate large quantities of transcript sequences for the purpose of gene discovery and functional genomic studies. The Ananas comosus var. bracteatus transcriptome was sequenced by the Illumina paired-end sequencing technology. We obtained a total of 23.5 million high quality sequencing reads, 1,555,808 contigs and 41,052 unigenes. In total 41,052 unigenes of Ananas comosus var. bracteatus, 23,275 unigenes were annotated in the NCBI non-redundant protein database and 23,134 unigenes were annotated in the Swiss-Port database. Out of these, 17,748 and 8,505 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Functional annotation against Kyoto Encyclopedia of Genes and Genomes Pathway database identified 5,825 unigenes which were mapped to 117 pathways. The assembly predicted many unigenes that were previously unknown. The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum. Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique. We predicted unigenes encoding enzymes involved in terpenoid and phenylpropanoid biosynthesis. The sequence data provide the most comprehensive transcriptomic resource currently available for Ananas comosus var. bracteatus. To our knowledge; this is the first report on the de novo transcriptome sequencing of the Ananas comosus var. bracteatus. Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus.

Transcriptome Sequence Analysis of an Ornamental Plant, Ananas comosus var. bracteatus, Revealed the Potential Unigenes Involved in Terpenoid and Phenylpropanoid Biosynthesis

PubMed Central

Ma, Jun; Kanakala, S.; He, Yehua; Zhang, Junli; Zhong, Xiaolan

2015-01-01

Background Ananas comosus var. bracteatus (Red Pineapple) is an important ornamental plant for its colorful leaves and decorative red fruits. Because of its complex genome, it is difficult to understand the molecular mechanisms involved in the growth and development. Thus high-throughput transcriptome sequencing of Ananas comosus var. bracteatus is necessary to generate large quantities of transcript sequences for the purpose of gene discovery and functional genomic studies. Results The Ananas comosus var. bracteatus transcriptome was sequenced by the Illumina paired-end sequencing technology. We obtained a total of 23.5 million high quality sequencing reads, 1,555,808 contigs and 41,052 unigenes. In total 41,052 unigenes of Ananas comosus var. bracteatus, 23,275 unigenes were annotated in the NCBI non-redundant protein database and 23,134 unigenes were annotated in the Swiss-Port database. Out of these, 17,748 and 8,505 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Functional annotation against Kyoto Encyclopedia of Genes and Genomes Pathway database identified 5,825 unigenes which were mapped to 117 pathways. The assembly predicted many unigenes that were previously unknown. The annotated unigenes were compared against pineapple, rice, maize, Arabidopsis, and sorghum. Unigenes that did not match any of those five sequence datasets are considered to be Ananas comosus var. bracteatus unique. We predicted unigenes encoding enzymes involved in terpenoid and phenylpropanoid biosynthesis. Conclusion The sequence data provide the most comprehensive transcriptomic resource currently available for Ananas comosus var. bracteatus. To our knowledge; this is the first report on the de novo transcriptome sequencing of the Ananas comosus var. bracteatus. Unigenes obtained in this study, may help improve future gene expression, genetic and genomics studies in Ananas comosus var. bracteatus. PMID:25769053

Autochthonous Hepatozoon infection in hunting dogs and foxes from the Czech Republic.

PubMed

Mitková, Barbora; Hrazdilová, Kristýna; Steinbauer, Vladimír; D'Amico, Gianluca; Mihalca, Andrei Daniel; Modrý, David

2016-11-01

Blood samples from 21 red foxes (Vulpes vulpes) and 8 hunting dogs from the same locality in the Czech Republic were examined for presence of Hepatozoon canis/Hepatozoon sp. The dogs were selected based on their close contact with foxes during fox bolting and because they had not traveled into known endemic areas. Using diagnostic PCR amplifying partial 18S rDNA fragment, Hepatozoon DNA was detected in 20 red foxes (95 %) and 4 dogs (50 %). From 8 positive foxes and 2 positive dogs, we obtained nearly complete 18S rDNA sequences. Phylogenetic analyses of these sequences revealed very low variability. Buffy coat smears from positive dogs were prepared and examined. No Hepatozoon gamonts were found. This study provides the first report of autochthonous infection of H. canis/Hepatozoon in dogs and foxes from the Czech Republic. Our study indirectly demonstrates cross infection between red foxes and dogs and confirms autochthonous infection of Hepatozoon canis in dogs living in a geographic area well outside the range of Rhipicephalus sanguineus sensu lato, which is so far the only known vector of H. canis in Europe.

Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.

PubMed

Matsuzaki, Motomichi; Misumi, Osami; Shin-I, Tadasu; Maruyama, Shinichiro; Takahara, Manabu; Miyagishima, Shin-Ya; Mori, Toshiyuki; Nishida, Keiji; Yagisawa, Fumi; Nishida, Keishin; Yoshida, Yamato; Nishimura, Yoshiki; Nakao, Shunsuke; Kobayashi, Tamaki; Momoyama, Yu; Higashiyama, Tetsuya; Minoda, Ayumi; Sano, Masako; Nomoto, Hisayo; Oishi, Kazuko; Hayashi, Hiroko; Ohta, Fumiko; Nishizaka, Satoko; Haga, Shinobu; Miura, Sachiko; Morishita, Tomomi; Kabeya, Yukihiro; Terasawa, Kimihiro; Suzuki, Yutaka; Ishii, Yasuyuki; Asakawa, Shuichi; Takano, Hiroyoshi; Ohta, Niji; Kuroiwa, Haruko; Tanaka, Kan; Shimizu, Nobuyoshi; Sugano, Sumio; Sato, Naoki; Nozaki, Hisayoshi; Ogasawara, Naotake; Kohara, Yuji; Kuroiwa, Tsuneyoshi

2004-04-08

Small, compact genomes of ultrasmall unicellular algae provide information on the basic and essential genes that support the lives of photosynthetic eukaryotes, including higher plants. Here we report the 16,520,305-base-pair sequence of the 20 chromosomes of the unicellular red alga Cyanidioschyzon merolae 10D as the first complete algal genome. We identified 5,331 genes in total, of which at least 86.3% were expressed. Unique characteristics of this genomic structure include: a lack of introns in all but 26 genes; only three copies of ribosomal DNA units that maintain the nucleolus; and two dynamin genes that are involved only in the division of mitochondria and plastids. The conserved mosaic origin of Calvin cycle enzymes in this red alga and in green plants supports the hypothesis of the existence of single primary plastid endosymbiosis. The lack of a myosin gene, in addition to the unexpressed actin gene, suggests a simpler system of cytokinesis. These results indicate that the C. merolae genome provides a model system with a simple gene composition for studying the origin, evolution and fundamental mechanisms of eukaryotic cells.

Identification of Paracoccidioides brasiliensis by gold nanoprobes

NASA Astrophysics Data System (ADS)

Martins, Jaciara F. S.; Castilho, Maiara L.; Cardoso, Maria A. G.; Carreiro, Andrea P.; Martin, Airton A.; Raniero, Leandro

2012-01-01

Paracoccidioides brasiliensis (P. brasiliensis) is a thermal dimorphic fungus and causal agent of paracoccidioidomycosis. Epidemiological data shows that it is mainly concentrated in Central and South America countries, with most registered cases in Colombia, Brazil, and Venezuela. The histopathological similarity with others fungal infection makes the diagnosis of P. brasiliensis more complicated. Therefore, the aim of this work was to find a positive and negative test for P. brasiliensis using gold nanoprobes as a new tool for P. brasiliensis detection. Gold nanoparticles were synthesized by reduction of gold chloride with sodium citrate. The results of this procedure is a wine-red solution with a maximum absorption in the range of ~520-530nm. A specific P. brasiliensis sequence of oligonucleotide was bonded to the nanoparticles, which maintained the wine-red color. The color changes from red to blue for negative diagnostic and is unchanged for a positive test. The H-bond interaction of DNA with the complementary DNA keeps strands together and forms double helical structure, maintaining the colloid stability. However, for non-complimentary DNA sequence the nanoprobes merge into a cluster, changing the light absorption.

Habitability of super-Earth planets around other suns: models including Red Giant Branch evolution.

PubMed

von Bloh, W; Cuntz, M; Schröder, K-P; Bounama, C; Franck, S

2009-01-01

The unexpected diversity of exoplanets includes a growing number of super-Earth planets, i.e., exoplanets with masses of up to several Earth masses and a similar chemical and mineralogical composition as Earth. We present a thermal evolution model for a 10 Earth-mass planet orbiting a star like the Sun. Our model is based on the integrated system approach, which describes the photosynthetic biomass production and takes into account a variety of climatological, biogeochemical, and geodynamical processes. This allows us to identify a so-called photosynthesis-sustaining habitable zone (pHZ), as determined by the limits of biological productivity on the planetary surface. Our model considers solar evolution during the main-sequence stage and along the Red Giant Branch as described by the most recent solar model. We obtain a large set of solutions consistent with the principal possibility of life. The highest likelihood of habitability is found for "water worlds." Only mass-rich water worlds are able to realize pHZ-type habitability beyond the stellar main sequence on the Red Giant Branch.

Emerging Perception of Causality in Action-and-Reaction Sequences from 4 to 6 Months of Age: Is It Domain-Specific?

ERIC Educational Resources Information Center

Schlottmann, Anne; Ray, Elizabeth D.; Surian, Luca

2012-01-01

Two experiments (N=136) studied how 4- to 6-month-olds perceive a simple schematic event, seen as goal-directed action and reaction from 3 years of age. In our causal reaction event, a red square moved toward a blue square, stopping prior to contact. Blue began to move away before red stopped, so that both briefly moved simultaneously at a…

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

PubMed Central

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. PMID:26089826

Approximate equiangular tight frames for compressed sensing and CDMA applications

NASA Astrophysics Data System (ADS)

Tsiligianni, Evaggelia; Kondi, Lisimachos P.; Katsaggelos, Aggelos K.

2017-12-01

Performance guarantees for recovery algorithms employed in sparse representations, and compressed sensing highlights the importance of incoherence. Optimal bounds of incoherence are attained by equiangular unit norm tight frames (ETFs). Although ETFs are important in many applications, they do not exist for all dimensions, while their construction has been proven extremely difficult. In this paper, we construct frames that are close to ETFs. According to results from frame and graph theory, the existence of an ETF depends on the existence of its signature matrix, that is, a symmetric matrix with certain structure and spectrum consisting of two distinct eigenvalues. We view the construction of a signature matrix as an inverse eigenvalue problem and propose a method that produces frames of any dimensions that are close to ETFs. Due to the achieved equiangularity property, the so obtained frames can be employed as spreading sequences in synchronous code-division multiple access (s-CDMA) systems, besides compressed sensing.

Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor

PubMed Central

O'Connell Motherway, Mary; Zomer, Aldert; Leahy, Sinead C.; Reunanen, Justus; Bottacini, Francesca; Claesson, Marcus J.; O'Brien, Frances; Flynn, Kiera; Casey, Patrick G.; Moreno Munoz, Jose Antonio; Kearney, Breda; Houston, Aileen M.; O'Mahony, Caitlin; Higgins, Des G.; Shanahan, Fergus; Palva, Airi; de Vos, Willem M.; Fitzgerald, Gerald F.; Ventura, Marco; O'Toole, Paul W.; van Sinderen, Douwe

2011-01-01

Development of the human gut microbiota commences at birth, with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date, the genetic basis of Bifidobacterium colonization and persistence remains poorly understood. Transcriptome analysis of the Bifidobacterium breve UCC2003 2.42-Mb genome in a murine colonization model revealed differential expression of a type IVb tight adherence (Tad) pilus-encoding gene cluster designated “tad2003.” Mutational analysis demonstrated that the tad2003 gene cluster is essential for efficient in vivo murine gut colonization, and immunogold transmission electron microscopy confirmed the presence of Tad pili at the poles of B. breve UCC2003 cells. Conservation of the Tad pilus-encoding locus among other B. breve strains and among sequenced Bifidobacterium genomes supports the notion of a ubiquitous pili-mediated host colonization and persistence mechanism for bifidobacteria. PMID:21690406

Identification of a rice gene (Bph 1) conferring resistance to brown planthopper (Nilaparvata lugens Stal) using STS markers.

PubMed

Kim, Suk-Man; Sohn, Jae-Keun

2005-08-31

This study was carried out to identify a high-resolution marker for a gene conferring resistance to brown planthopper (BPH) biotype 1, using japonica type resistant lines. Bulked segregant analyses were conducted using 520 RAPD primers to identify RAPD fragments linked to the BPH resistance gene. Eleven RAPDs were shown to be polymorphic amplicons between resistant and susceptible progeny. One of these primers, OPE 18, which amplified a 923 bp band tightly linked to resistance, was converted into a sequence-tagged-site (STS) marker. The STS marker, BpE18-3, was easily detectable as a dominant band with tight linkage (3.9cM) to Bph1. It promises to be useful as a marker for assisted selection of resistant progeny in backcross breeding programs to introgress the resistance gene into elite japonica cultivars.

Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor.

PubMed

O'Connell Motherway, Mary; Zomer, Aldert; Leahy, Sinead C; Reunanen, Justus; Bottacini, Francesca; Claesson, Marcus J; O'Brien, Frances; Flynn, Kiera; Casey, Patrick G; Munoz, Jose Antonio Moreno; Kearney, Breda; Houston, Aileen M; O'Mahony, Caitlin; Higgins, Des G; Shanahan, Fergus; Palva, Airi; de Vos, Willem M; Fitzgerald, Gerald F; Ventura, Marco; O'Toole, Paul W; van Sinderen, Douwe

2011-07-05

Development of the human gut microbiota commences at birth, with bifidobacteria being among the first colonizers of the sterile newborn gastrointestinal tract. To date, the genetic basis of Bifidobacterium colonization and persistence remains poorly understood. Transcriptome analysis of the Bifidobacterium breve UCC2003 2.42-Mb genome in a murine colonization model revealed differential expression of a type IVb tight adherence (Tad) pilus-encoding gene cluster designated "tad(2003)." Mutational analysis demonstrated that the tad(2003) gene cluster is essential for efficient in vivo murine gut colonization, and immunogold transmission electron microscopy confirmed the presence of Tad pili at the poles of B. breve UCC2003 cells. Conservation of the Tad pilus-encoding locus among other B. breve strains and among sequenced Bifidobacterium genomes supports the notion of a ubiquitous pili-mediated host colonization and persistence mechanism for bifidobacteria.

Comparison of de novo assembly statistics of Cucumis sativus L.

NASA Astrophysics Data System (ADS)

Wojcieszek, Michał; Kuśmirek, Wiktor; Pawełkowicz, Magdalena; PlÄ der, Wojciech; Nowak, Robert M.

2017-08-01

Genome sequencing is the core of genomic research. With the development of NGS and lowering the cost of procedure there is another tight gap - genome assembly. Developing the proper tool for this task is essential as quality of genome has important impact on further research. Here we present comparison of several de Bruijn assemblers tested on C. sativus genomic reads. The assessment shows that newly developed software - dnaasm provides better results in terms of quantity and quality. The number of generated sequences is lower by 5 - 33% with even two fold higher N50. Quality check showed reliable results were generated by dnaasm. This provides us with very strong base for future genomic analysis.

Identification and characterization of Burkholderia multivorans CCA53.

PubMed

Akita, Hironaga; Kimura, Zen-Ichiro; Yusoff, Mohd Zulkhairi Mohd; Nakashima, Nobutaka; Hoshino, Tamotsu

2017-07-06

A lignin-degrading bacterium, Burkholderia sp. CCA53, was previously isolated from leaf soil. The purpose of this study was to determine phenotypic and biochemical features of Burkholderia sp. CCA53. Multilocus sequence typing (MLST) analysis based on fragments of the atpD, gltD, gyrB, lepA, recA and trpB gene sequences was performed to identify Burkholderia sp. CCA53. The MLST analysis revealed that Burkholderia sp. CCA53 was tightly clustered with B. multivorans ATCC BAA-247 T . The quinone and cellular fatty acid profiles, carbon source utilization, growth temperature and pH were consistent with the characteristics of B. multivorans species. Burkholderia sp. CCA53 was therefore identified as B. multivorans CCA53.

Periodic, chaotic, and doubled earthquake recurrence intervals on the deep San Andreas Fault

USGS Publications Warehouse

Shelly, David R.

2010-01-01

Earthquake recurrence histories may provide clues to the timing of future events, but long intervals between large events obscure full recurrence variability. In contrast, small earthquakes occur frequently, and recurrence intervals are quantifiable on a much shorter time scale. In this work, I examine an 8.5-year sequence of more than 900 recurring low-frequency earthquake bursts composing tremor beneath the San Andreas fault near Parkfield, California. These events exhibit tightly clustered recurrence intervals that, at times, oscillate between ~3 and ~6 days, but the patterns sometimes change abruptly. Although the environments of large and low-frequency earthquakes are different, these observations suggest that similar complexity might underlie sequences of large earthquakes.

Distal alluvial fan sediments in early Proterozoic red beds of the Wilgerivier formation, Waterberg Group, South Africa

NASA Astrophysics Data System (ADS)

Van Der Neut, M.; Eriksson, P. G.; Callaghan, C. C.

The 1900 - 1700 M.a. Waterberg Group belongs to a series of southern African cratonic cover sequences of roughly equivalent age. Red beds of the Wilgerivier Formation comprise sandstones, interbedded with subordinate conglomerates and minor mudrocks. These immature sedimentary rocks exhibit lenticular bedding, radial palaeocurrent patterns and features indicative of both streamflow and gravity-flow deposition. A distal wet alluvial fan palaeoenvironmental setting is envisaged, with fan-deltas forming where alluvial lobes prograded into a lacustrine basin. Intrastratal, diagenetic alteration of ferromagnesian detrital grains and ferruginous grain coatings led to the red colouration of the Wilgerivier sediments.

First description of Grapevine leafroll-associated virus 5 in Argentina and partial genome sequence.

PubMed

Gómez Talquenca, Sebastián; Muñoz, Claudio; Grau, Oscar; Gracia, Olga

2009-02-01

An accession of Vitis vinifera cv. Red Globe from Argentina, was found to be infected with Grapevine leafroll-associated virus-5 by ELISA. It was partially sequenced, and three ORFs, corresponding to HSP70h, HSP90h, and CP, were found. This isolate shares a high aminoacid identity with the previously reported sequence of the virus, and identities between 80% and 90% with previously reported GLRaV-9 and GLRaV-4 isolates. The analysis of the sequence supports the clustering together with GLRaV-4 and GLRV-9 inside the Ampelovirus genus.

Application of genetic algorithm in integrated setup planning and operation sequencing

NASA Astrophysics Data System (ADS)

Kafashi, Sajad; Shakeri, Mohsen

2011-01-01

Process planning is an essential component for linking design and manufacturing process. Setup planning and operation sequencing is two main tasks in process planning. Many researches solved these two problems separately. Considering the fact that the two functions are complementary, it is necessary to integrate them more tightly so that performance of a manufacturing system can be improved economically and competitively. This paper present a generative system and genetic algorithm (GA) approach to process plan the given part. The proposed approach and optimization methodology analyses the TAD (tool approach direction), tolerance relation between features and feature precedence relations to generate all possible setups and operations using workshop resource database. Based on these technological constraints the GA algorithm approach, which adopts the feature-based representation, optimizes the setup plan and sequence of operations using cost indices. Case study show that the developed system can generate satisfactory results in optimizing the setup planning and operation sequencing simultaneously in feasible condition.

Of macrophages and red blood cells; a complex love story.

PubMed

de Back, Djuna Z; Kostova, Elena B; van Kraaij, Marian; van den Berg, Timo K; van Bruggen, Robin

2014-01-01

Macrophages tightly control the production and clearance of red blood cells (RBC). During steady state hematopoiesis, approximately 10(10) RBC are produced per hour within erythroblastic islands in humans. In these erythroblastic islands, resident bone marrow macrophages provide erythroblasts with interactions that are essential for erythroid development. New evidence suggests that not only under homeostasis but also under stress conditions, macrophages play an important role in promoting erythropoiesis. Once RBC have matured, these cells remain in circulation for about 120 days. At the end of their life span, RBC are cleared by macrophages residing in the spleen and the liver. Current theories about the removal of senescent RBC and the essential role of macrophages will be discussed as well as the role of macrophages in facilitating the removal of damaged cellular content from the RBC. In this review we will provide an overview on the role of macrophages in the regulation of RBC production, maintenance and clearance. In addition, we will discuss the interactions between these two cell types during transfer of immune complexes and pathogens from RBC to macrophages.

Ancient genomics

PubMed Central

Der Sarkissian, Clio; Allentoft, Morten E.; Ávila-Arcos, María C.; Barnett, Ross; Campos, Paula F.; Cappellini, Enrico; Ermini, Luca; Fernández, Ruth; da Fonseca, Rute; Ginolhac, Aurélien; Hansen, Anders J.; Jónsson, Hákon; Korneliussen, Thorfinn; Margaryan, Ashot; Martin, Michael D.; Moreno-Mayar, J. Víctor; Raghavan, Maanasa; Rasmussen, Morten; Velasco, Marcela Sandoval; Schroeder, Hannes; Schubert, Mikkel; Seguin-Orlando, Andaine; Wales, Nathan; Gilbert, M. Thomas P.; Willerslev, Eske; Orlando, Ludovic

2015-01-01

The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past. PMID:25487338

SDSS-IV MaNGA: Spatially Resolved Star Formation Main Sequence and LI(N)ER Sequence

NASA Astrophysics Data System (ADS)

Hsieh, B. C.; Lin, Lihwai; Lin, J. H.; Pan, H. A.; Hsu, C. H.; Sánchez, S. F.; Cano-Díaz, M.; Zhang, K.; Yan, R.; Barrera-Ballesteros, J. K.; Boquien, M.; Riffel, R.; Brownstein, J.; Cruz-González, I.; Hagen, A.; Ibarra, H.; Pan, K.; Bizyaev, D.; Oravetz, D.; Simmons, A.

2017-12-01

We present our study on the spatially resolved Hα and M * relation for 536 star-forming and 424 quiescent galaxies taken from the MaNGA survey. We show that the star formation rate surface density ({{{Σ }}}{SFR}), derived based on the Hα emissions, is strongly correlated with the M * surface density ({{{Σ }}}* ) on kiloparsec scales for star-forming galaxies and can be directly connected to the global star-forming sequence. This suggests that the global main sequence may be a consequence of a more fundamental relation on small scales. On the other hand, our result suggests that ∼20% of quiescent galaxies in our sample still have star formation activities in the outer region with lower specific star formation rate (SSFR) than typical star-forming galaxies. Meanwhile, we also find a tight correlation between {{{Σ }}}{{H}α } and {{{Σ }}}* for LI(N)ER regions, named the resolved “LI(N)ER” sequence, in quiescent galaxies, which is consistent with the scenario that LI(N)ER emissions are primarily powered by the hot, evolved stars as suggested in the literature.

Analysis of delay reducing and fuel saving sequencing and spacing algorithms for arrival traffic

NASA Technical Reports Server (NTRS)

Neuman, Frank; Erzberger, Heinz

1991-01-01

The air traffic control subsystem that performs sequencing and spacing is discussed. The function of the sequencing and spacing algorithms is to automatically plan the most efficient landing order and to assign optimally spaced landing times to all arrivals. Several algorithms are described and their statistical performance is examined. Sequencing brings order to an arrival sequence for aircraft. First-come-first-served sequencing (FCFS) establishes a fair order, based on estimated times of arrival, and determines proper separations. Because of the randomness of the arriving traffic, gaps will remain in the sequence of aircraft. Delays are reduced by time-advancing the leading aircraft of each group while still preserving the FCFS order. Tightly spaced groups of aircraft remain with a mix of heavy and large aircraft. Spacing requirements differ for different types of aircraft trailing each other. Traffic is reordered slightly to take advantage of this spacing criterion, thus shortening the groups and reducing average delays. For heavy traffic, delays for different traffic samples vary widely, even when the same set of statistical parameters is used to produce each sample. This report supersedes NASA TM-102795 on the same subject. It includes a new method of time-advance as well as an efficient method of sequencing and spacing for two dependent runways.

Campbell's monkeys concatenate vocalizations into context-specific call sequences

PubMed Central

Ouattara, Karim; Lemasson, Alban; Zuberbühler, Klaus

2009-01-01

Primate vocal behavior is often considered irrelevant in modeling human language evolution, mainly because of the caller's limited vocal control and apparent lack of intentional signaling. Here, we present the results of a long-term study on Campbell's monkeys, which has revealed an unrivaled degree of vocal complexity. Adult males produced six different loud call types, which they combined into various sequences in highly context-specific ways. We found stereotyped sequences that were strongly associated with cohesion and travel, falling trees, neighboring groups, nonpredatory animals, unspecific predatory threat, and specific predator classes. Within the responses to predators, we found that crowned eagles triggered four and leopards three different sequences, depending on how the caller learned about their presence. Callers followed a number of principles when concatenating sequences, such as nonrandom transition probabilities of call types, addition of specific calls into an existing sequence to form a different one, or recombination of two sequences to form a third one. We conclude that these primates have overcome some of the constraints of limited vocal control by combinatorial organization. As the different sequences were so tightly linked to specific external events, the Campbell's monkey call system may be the most complex example of ‘proto-syntax’ in animal communication known to date. PMID:20007377

Mining a database of single amplified genomes from Red Sea brine pool extremophiles—improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA)

PubMed Central

Grötzinger, Stefan W.; Alam, Intikhab; Ba Alawi, Wail; Bajic, Vladimir B.; Stingl, Ulrich; Eppinger, Jörg

2014-01-01

Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile's genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available through the INDIGO website. PMID:24778629

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

Thilker, David A.; Bianchi, Luciana; Schiminovich, David

We have discovered recent star formation in the outermost portion ((1-4) x R {sub 25}) of the nearby lenticular (S0) galaxy NGC 404 using Galaxy Evolution Explorer UV imaging. FUV-bright sources are strongly concentrated within the galaxy's H I ring (formed by a merger event according to del RIo et al.), even though the average gas density is dynamically subcritical. Archival Hubble Space Telescope imaging reveals resolved upper main-sequence stars and conclusively demonstrates that the UV light originates from recent star formation activity. We present FUV, NUV radial surface brightness profiles, and integrated magnitudes for NGC 404. Within the ring,more » the average star formation rate (SFR) surface density ({Sigma}{sub SFR}) is {approx}2.2 x 10{sup -5} M {sub sun} yr{sup -1} kpc{sup -2}. Of the total FUV flux, 70% comes from the H I ring which is forming stars at a rate of 2.5 x 10{sup -3} M {sub sun} yr{sup -1}. The gas consumption timescale, assuming a constant SFR and no gas recycling, is several times the age of the universe. In the context of the UV-optical galaxy color-magnitude diagram, the presence of the star-forming H I ring places NGC 404 in the green valley separating the red and blue sequences. The rejuvenated lenticular galaxy has experienced a merger-induced, disk-building excursion away from the red sequence toward bluer colors, where it may evolve quiescently or (if appropriately triggered) experience a burst capable of placing it on the blue/star-forming sequence for up to {approx}1 Gyr. The green valley galaxy population is heterogeneous, with most systems transitioning from blue to red but others evolving in the opposite sense due to acquisition of fresh gas through various channels.« less

Structure of the red fluorescent protein from a lancelet (Branchiostoma lanceolatum): a novel GYG chromophore covalently bound to a nearby tyrosine

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

Pletnev, Vladimir Z., E-mail: vzpletnev@gmail.com; Pletneva, Nadya V.; Lukyanov, Konstantin A.

The crystal structure of the novel red emitting fluorescent protein from lancelet Branchiostoma lanceolatum (Chordata) revealed an unusual five residues cyclic unit comprising Gly58-Tyr59-Gly60 chromophore, the following Phe61 and Tyr62 covalently bound to chromophore Tyr59. A key property of proteins of the green fluorescent protein (GFP) family is their ability to form a chromophore group by post-translational modifications of internal amino acids, e.g. Ser65-Tyr66-Gly67 in GFP from the jellyfish Aequorea victoria (Cnidaria). Numerous structural studies have demonstrated that the green GFP-like chromophore represents the ‘core’ structure, which can be extended in red-shifted proteins owing to modifications of the protein backbonemore » at the first chromophore-forming position. Here, the three-dimensional structures of green laGFP (λ{sub ex}/λ{sub em} = 502/511 nm) and red laRFP (λ{sub ex}/λ{sub em} ≃ 521/592 nm), which are fluorescent proteins (FPs) from the lancelet Branchiostoma lanceolatum (Chordata), were determined together with the structure of a red variant laRFP-ΔS83 (deletion of Ser83) with improved folding. Lancelet FPs are evolutionarily distant and share only ∼20% sequence identity with cnidarian FPs, which have been extensively characterized and widely used as genetically encoded probes. The structure of red-emitting laRFP revealed three exceptional features that have not been observed in wild-type fluorescent proteins from Cnidaria reported to date: (i) an unusual chromophore-forming sequence Gly58-Tyr59-Gly60, (ii) the presence of Gln211 at the position of the conserved catalytic Glu (Glu222 in Aequorea GFP), which proved to be crucial for chromophore formation, and (iii) the absence of modifications typical of known red chromophores and the presence of an extremely unusual covalent bond between the Tyr59 C{sup β} atom and the hydroxyl of the proximal Tyr62. The impact of this covalent bond on the red emission and the large Stokes shift (∼70 nm) of laRFP was verified by extensive structure-based site-directed mutagenesis.« less

De Novo Assembly and Comparative Transcriptome Analyses of Red and Green Morphs of Sweet Basil Grown in Full Sunlight.

PubMed

Torre, Sara; Tattini, Massimiliano; Brunetti, Cecilia; Guidi, Lucia; Gori, Antonella; Marzano, Cristina; Landi, Marco; Sebastiani, Federico

2016-01-01

Sweet basil (Ocimum basilicum), one of the most popular cultivated herbs worldwide, displays a number of varieties differing in several characteristics, such as the color of the leaves. The development of a reference transcriptome for sweet basil, and the analysis of differentially expressed genes in acyanic and cyanic cultivars exposed to natural sunlight irradiance, has interest from horticultural and biological point of views. There is still great uncertainty about the significance of anthocyanins in photoprotection, and how green and red morphs may perform when exposed to photo-inhibitory light, a condition plants face on daily and seasonal basis. We sequenced the leaf transcriptome of the green-leaved Tigullio (TIG) and the purple-leaved Red Rubin (RR) exposed to full sunlight over a four-week experimental period. We assembled and annotated 111,007 transcripts. A total of 5,468 and 5,969 potential SSRs were identified in TIG and RR, respectively, out of which 66 were polymorphic in silico. Comparative analysis of the two transcriptomes showed 2,372 differentially expressed genes (DEGs) clustered in 222 enriched Gene ontology terms. Green and red basil mostly differed for transcripts abundance of genes involved in secondary metabolism. While the biosynthesis of waxes was up-regulated in red basil, the biosynthesis of flavonols and carotenoids was up-regulated in green basil. Data from our study provides a comprehensive transcriptome survey, gene sequence resources and microsatellites that can be used for further investigations in sweet basil. The analysis of DEGs and their functional classification also offers new insights on the functional role of anthocyanins in photoprotection.

Reconstructing the history of a fragmented and heavily exploited red deer population using ancient and contemporary DNA.

PubMed

Rosvold, Jørgen; Røed, Knut H; Hufthammer, Anne Karin; Andersen, Reidar; Stenøien, Hans K

2012-09-26

Red deer (Cervus elaphus) have been an important human resource for millennia, experiencing intensive human influence through habitat alterations, hunting and translocation of animals. In this study we investigate a time series of ancient and contemporary DNA from Norwegian red deer spanning about 7,000 years. Our main aim was to investigate how increasing agricultural land use, hunting pressure and possibly human mediated translocation of animals have affected the genetic diversity on a long-term scale. We obtained mtDNA (D-loop) sequences from 73 ancient specimens. These show higher genetic diversity in ancient compared to extant samples, with the highest diversity preceding the onset of agricultural intensification in the Early Iron Age. Using standard diversity indices, Bayesian skyline plot and approximate Bayesian computation, we detected a population reduction which was more prolonged than, but not as severe as, historic documents indicate. There are signs of substantial changes in haplotype frequencies primarily due to loss of haplotypes through genetic drift. There is no indication of human mediated translocations into the Norwegian population. All the Norwegian sequences show a western European origin, from which the Norwegian lineage diverged approximately 15,000 years ago. Our results provide direct insight into the effects of increasing habitat fragmentation and human hunting pressure on genetic diversity and structure of red deer populations. They also shed light on the northward post-glacial colonisation process of red deer in Europe and suggest increased precision in inferring past demographic events when including both ancient and contemporary DNA.

Molecular recognition of pyr mRNA by the Bacillus subtilis attenuation regulatory protein PyrR

PubMed Central

Bonner, Eric R.; D’Elia, John N.; Billips, Benjamin K.; Switzer, Robert L.

2001-01-01

The pyrimidine nucleotide biosynthesis (pyr) operon in Bacillus subtilis is regulated by transcriptional attenuation. The PyrR protein binds in a uridine nucleotide-dependent manner to three attenuation sites at the 5′-end of pyr mRNA. PyrR binds an RNA-binding loop, allowing a terminator hairpin to form and repressing the downstream genes. The binding of PyrR to defined RNA molecules was characterized by a gel mobility shift assay. Titration indicated that PyrR binds RNA in an equimolar ratio. PyrR bound more tightly to the binding loops from the second (BL2 RNA) and third (BL3 RNA) attenuation sites than to the binding loop from the first (BL1 RNA) attenuation site. PyrR bound BL2 RNA 4–5-fold tighter in the presence of saturating UMP or UDP and 150- fold tighter with saturating UTP, suggesting that UTP is the more important co-regulator. The minimal RNA that bound tightly to PyrR was 28 nt long. Thirty-one structural variants of BL2 RNA were tested for PyrR binding affinity. Two highly conserved regions of the RNA, the terminal loop and top of the upper stem and a purine-rich internal bulge and the base pairs below it, were crucial for tight binding. Conserved elements of RNA secondary structure were also required for tight binding. PyrR protected conserved areas of the binding loop in hydroxyl radical footprinting experiments. PyrR likely recognizes conserved RNA sequences, but only if they are properly positioned in the correct secondary structure. PMID:11726695

Molecular dynamics study of biodegradation of azo dyes via their interactions with AzrC azoreductase.

PubMed

Haghshenas, Hamed; Kay, Maryam; Dehghanian, Fariba; Tavakol, Hossein

2016-01-01

Azo dyes are one of the most important class of dyes, which have been widely used in industries. Because of the environmental pollution of azo dyes, many studies have been performed to study their biodegradation using bacterial systems. In present work, the AzrC of mesophilic gram-positive Bacillus sp. B29 has been considered to study its interaction with five common azo dyes (orange G, acid red 88, Sudan I, orange I, and methyl red). The molecular dynamics simulations have been employed to study the interaction between AzrC and azo dyes. The trajectory was confirmed using root mean square deviation and the root mean square fluctuation analyses. Then, the hydrogen bond and alanine scanning analyses were performed to reveal active site residues. Phe105 (A), Phe125 (B), Phe172 (B), and Pro132 (B) have been found as the most important hydrophobic residues whereas Asn104 (A), Tyr127 (B), and Asn187 (A) have key role in making hydrogen bond. The results of molecular mechanics Poisson-Boltzmann surface area and molecular mechanics generalized Born surface area calculations proved that the hydrophobic azo dyes like Acid red 88 binds more tightly to the AzrC protein. The calculated data suggested MR A 121 (B) I as a potential candidate for improving the AzrC-MR interactions.

Recovering the systemic redshift of galaxies from their Lyman alpha line profile

NASA Astrophysics Data System (ADS)

Verhamme, A.; Garel, T.; Ventou, E.; Contini, T.; Bouché, N.; Herenz, EC; Richard, J.; Bacon, R.; Schmidt, KB; Maseda, M.; Marino, RA; Brinchmann, J.; Cantalupo, S.; Caruana, J.; Clément, B.; Diener, C.; Drake, AB; Hashimoto, T.; Inami, H.; Kerutt, J.; Kollatschny, W.; Leclercq, F.; Patrício, V.; Schaye, J.; Wisotzki, L.; Zabl, J.

2018-07-01

The Lyman alpha (Ly α) line of Hydrogen is a prominent feature in the spectra of star-forming galaxies, usually redshifted by a few hundreds of km s-1 compared to the systemic redshift. This large offset hampers follow-up surveys, galaxy pair statistics, and correlations with quasar absorption lines when only Ly α is available. We propose diagnostics that can be used to recover the systemic redshift directly from the properties of the Ly α line profile. We use spectroscopic observations of Ly α emitters for which a precise measurement of the systemic redshift is available. Our sample contains 13 sources detected between z ≈ 3 and z ≈ 6 as part of various multi-unit spectroscopic explorer guaranteed time observations. We also include a compilation of spectroscopic Ly α data from the literature spanning a wide redshift range (z ≈ 0-8). First, restricting our analysis to double-peaked Ly α spectra, we find a tight correlation between the velocity offset of the red peak with respect to the systemic redshift, V_peak^red, and the separation of the peaks. Secondly, we find a correlation between V_peak^red and the full width at half-maximum of the Ly α line. Fitting formulas to estimate systemic redshifts of galaxies with an accuracy of ≤100 km s-1, when only the Ly α emission line is available, are given for the two methods.

Messier 101 Single Orbit Exposure

NASA Image and Video Library

2003-07-25

This single orbit exposure, ultraviolet color image of Messier 101 was taken by NASA's Galaxy Evolution Explorer on June 20, 2003. Messier 101 is a large spiral galaxy located 20 million light-years from Earth. This image is a short and medium "exposure" picture of the evolution of star formation in a spiral galaxy. The far ultraviolet emission detects the younger stars as concentrated in tight spiral arms, while the near ultraviolet emission, which traces stars living for more than 100 million years, displays the movement of the spiral pattern over a 100 million year period. The red stars in the foreground of the image are Milky Way stars. http://photojournal.jpl.nasa.gov/catalog/PIA04632

Depositional and diagenetic models of some miocene evaporites on the Red Sea coast, Egypt

NASA Astrophysics Data System (ADS)

El Sayed A. A., Youssef

1986-06-01

The Miocene evaporites on the Red Sea coast, Egypt, are interpreted as a sabkha-chenier complex, which includes deposition in shallow water as well as in supratidal environments Costal sabkhas and shallow subaqueous evaporite sequences are recognised. The subaqueous sequence is represented by nodular mosaic and massive crystalline gypsum covered by a surface layer of nodular, white, dense powdery anhydrite. The sabkha sequences are represented by (a) small mounds overlying the older rock unit (Gebel El Rusas Formation) composed of fenestral stromatolitic and nodular dolomites overlain by a dolomitic limestone layer, (b) thin layer overlying the subaqueous evaporite sequence and composed of fenestral stromatolitic dolomite overlain by a nodular anhydrite layer. The nodular structure in the subaqueous as well as the sabkha sequences is formed diagenetically by transformation and recrystallization process. The dolomites in both sabkha sequences (a and b) are characterised by low Na + concentrations (143 to 755 ppm) and low values of δ 18O (- 1.85 to -8.7‰ PDB). This indicates that the dolomites were formed from saline water mixed with fresh water. These dolomites are also characterised by a low δ 13C (-12.95 to -27.1‰ PDB). This shows that the light carbon produced by the degradation of organic matter through the sulphate reduction process has played a significant role in the formation of these dolomites. Both microcrystalline and megacrystalline white dolomites are recognised in sabkha sequences. Relatively high concentrations of lead, zinc and copper are associated with the high percent of megacrystalline white dolomite.

The population of single and binary white dwarfs of the Galactic bulge

NASA Astrophysics Data System (ADS)

Torres, S.; García-Berro, E.; Cojocaru, R.; Calamida, A.

2018-05-01

Recent Hubble Space Telescope observations have unveiled the white dwarf cooling sequence of the Galactic bulge. Although the degenerate sequence can be well fitted employing the most up-to-date theoretical cooling sequences, observations show a systematic excess of red objects that cannot be explained by the theoretical models of single carbon-oxygen white dwarfs of the appropriate masses. Here, we present a population synthesis study of the white dwarf cooling sequence of the Galactic bulge that takes into account the populations of both single white dwarfs and binary systems containing at least one white dwarf. These calculations incorporate state-of-the-art cooling sequences for white dwarfs with hydrogen-rich and hydrogen-deficient atmospheres, for both white dwarfs with carbon-oxygen and helium cores, and also take into account detailed prescriptions of the evolutionary history of binary systems. Our Monte Carlo simulator also incorporates all the known observational biases. This allows us to model with a high degree of realism the white dwarf population of the Galactic bulge. We find that the observed excess of red stars can be partially attributed to white dwarf plus main sequence binaries, and to cataclysmic variables or dwarf novae. Our best fit is obtained with a higher binary fraction and an initial mass function slope steeper than standard values, as well as with the inclusion of differential reddening and blending. Our results also show that the possible contribution of double degenerate systems or young and thick-discbulge stars is negligible.

Metal-poor stars. IV - The evolution of red giants.

NASA Technical Reports Server (NTRS)

Rood, R. T.

1972-01-01

Detailed evolutionary calculations for six Population-II red giants are presented. The first five of these models are followed from the zero age main sequence to the onset of the helium flash. The sixth model allows the effect of direct electron-neutrino interactions to be estimated. The updated input physics and evolutionary code are described briefly. The results of the calculations are presented in a manner pertinent to later stages of evolutions and suitable for comparison with observations.

Preliminary characterisation of Pentlands paramyxovirus-1, -2 and -3, three new paramyxoviruses of rodents.

PubMed

Brooks, Fiona; Wood, Ann R; Thomson, Jackie; Deane, David; Everest, David J; McInnes, Colin J

2014-06-04

A paramyxovirus was discovered by chance during the primary culture of grey squirrel (Sciurus carolinensis) kidney cells from the UK. Amplification, sequencing and phylogenetic analysis of part of the genome encoding a region of the RNA polymerase (L gene) confirmed that the virus was a member of the Paramyxovirinae subfamily, but that it did not partition with any of the currently recognised paramyxovirus genera and instead segregated with the unclassified rodent viruses, J-virus, Beilong virus and Tailam virus as well as paramyxoviruses recently detected in rodents in Africa. A subsequent examination of kidney samples from red squirrels (Sciurus vulgaris) revealed that they too harboured a paramyxovirus, but sequence analysis of the corresponding region of the L gene revealed that it was approximately 67% identical to the grey squirrel virus, suggesting the presence of a second species of virus. In addition, one of the red squirrels examined harboured a second virus with approximately 69% identity to the grey squirrel virus, but only approximately 63% identity to the other red squirrel viruses, signifying the presence of a third species of paramyxovirus. In a sample of 22 red and grey squirrels 68% of those examined were found to harbour virus suggesting that paramyxovirus infection in squirrels may be common within the UK. Copyright © 2014 Elsevier B.V. All rights reserved.

DUST-CORRECTED COLORS REVEAL BIMODALITY IN THE HOST-GALAXY COLORS OF ACTIVE GALACTIC NUCLEI AT z {approx} 1

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

Cardamone, Carolin N.; Megan Urry, C.; Brammer, Gabriel

2010-09-20

Using new, highly accurate photometric redshifts from the MUSYC medium-band survey in the Extended Chandra Deep Field-South (ECDF-S), we fit synthetic stellar population models to compare active galactic nucleus (AGN) host galaxies to inactive galaxies at 0.8 {<=} z {<=} 1.2. We find that AGN host galaxies are predominantly massive galaxies on the red sequence and in the green valley of the color-mass diagram. Because both passive and dusty galaxies can appear red in optical colors, we use rest-frame near-infrared colors to separate passively evolving stellar populations from galaxies that are reddened by dust. As with the overall galaxy population,more » {approx}25% of the 'red' AGN host galaxies and {approx}75% of the 'green' AGN host galaxies have colors consistent with young stellar populations reddened by dust. The dust-corrected rest-frame optical colors are the blue colors of star-forming galaxies, which imply that these AGN hosts are not passively aging to the red sequence. At z {approx} 1, AGN activity is roughly evenly split between two modes of black hole growth: the first in passively evolving host galaxies, which may be heating up the galaxy's gas and preventing future episodes of star formation, and the second in dust-reddened young galaxies, which may be ionizing the galaxy's interstellar medium and shutting down star formation.« less

Galaxy Zoo: Major Galaxy Mergers Are Not a Significant Quenching Pathway

NASA Astrophysics Data System (ADS)

Weigel, Anna K.; Schawinski, Kevin; Caplar, Neven; Carpineti, Alfredo; Hart, Ross E.; Kaviraj, Sugata; Keel, William C.; Kruk, Sandor J.; Lintott, Chris J.; Nichol, Robert C.; Simmons, Brooke D.; Smethurst, Rebecca J.

2017-08-01

We use stellar mass functions to study the properties and the significance of quenching through major galaxy mergers. In addition to SDSS DR7 and Galaxy Zoo 1 data, we use samples of visually selected major galaxy mergers and post-merger galaxies. We determine the stellar mass functions of the stages that we would expect major-merger-quenched galaxies to pass through on their way from the blue cloud to the red sequence: (1) major merger, (2) post-merger, (3) blue early type, (4) green early type, and (5) red early type. Based on their similar mass function shapes, we conclude that major mergers are likely to form an evolutionary sequence from star formation to quiescence via quenching. Relative to all blue galaxies, the major-merger fraction increases as a function of stellar mass. Major-merger quenching is inconsistent with the mass and environment quenching model. At z˜ 0, major-merger-quenched galaxies are unlikely to constitute the majority of galaxies that transition through the green valley. Furthermore, between z˜ 0-0.5, major-merger-quenched galaxies account for 1%-5% of all quenched galaxies at a given stellar mass. Major galaxy mergers are therefore not a significant quenching pathway, neither at z˜ 0 nor within the last 5 Gyr. The majority of red galaxies must have been quenched through an alternative quenching mechanism that causes a slow blue to red evolution. .

Applications of three DNA barcodes in assorting intertidal red macroalgal flora in Qingdao, China

NASA Astrophysics Data System (ADS)

Zhao, Xiaobo; Pang, Shaojun; Shan, Tifeng; Liu, Feng

2013-03-01

This study is part of the endeavor to construct a comprehensive DNA barcoding database for common seaweeds in China. Identifications of red seaweeds, which have simple morphology and anatomy, are sometimes difficult solely depending on morphological characteristics. In recent years, DNA barcode technique has become a more and more effective tool to help solve some of the taxonomic difficulties. Some DNA markers such as COI (cytochrome oxidase subunit I) are proposed as standardized DNA barcodes for all seaweed species. In this study, COI, UPA (universal plastid amplicon, domain V of 23S rRNA), and ITS (nuclear internal transcribed spacer) were employed to analyze common species of intertidal red seaweeds in Qingdao (119.3°-121°E, 35.35°-37.09°N). The applicability of using one or a few combined barcodes to identify red seaweed species was tested. The results indicated that COI is a sensitive marker at species level. However, not all the tested species gave PCR amplification products due to lack of the universal primers. The second barcode UPA had effective universal primers but needed to be tested for the effectiveness of resolving closely related species. More than one ITS sequence types were found in some species in this investigation, which might lead to confusion in further analysis. Therefore ITS sequence is not recommended as a universal barcode for seaweeds identification.

Draft genome sequence of Xylella fastidiosa supsp. multiplex strain Griffin-1 from Quercus rubra in Georgia

USDA-ARS?s Scientific Manuscript database

The draft genome sequence of Xylella fastidiosa subsp. multiplex Strain Griffin-1 isolated from a red oak tree (Quercus rubra) in Georgia, U.S.A. is reported. The bacterium has a genome size of 2,387,314 bp with 51.7% G+C content and comprises 2,903 predicted open reading frames (ORFs), and 50 RNA g...

Draft Genome Sequence of a Red-Pigmented Janthinobacterium sp. Native to the Hudson Valley Watershed

PubMed Central

O’Brien, Kelsey

2018-01-01

ABSTRACT Water samples from the Hudson Valley watershed indicate that the area is host to many violacein-producing bacterial isolates. Here, we report the draft whole-genome sequence of Janthinobacterium sp. strain BJB412, an isolate lacking violacein production yet containing genes responsible for prodigiosin, biofilm production, and quorum sensing, like its purple-pigmented counterparts. PMID:29301893

Complete genome sequence of Yersinia ruckeri str. CSF007-82, etiologic agent of enteric redmouth disease in salmonid fish

USDA-ARS?s Scientific Manuscript database

We present the complete, closed and finished chromosomal and extra-chromosomal genome sequences of Y. ruckeri strain CSF007-82, etiologic agent of enteric red mouth disease in salmonid fish. The chromosome is 3,799,036 bp with a G+C content of 47.5% and encodes 3,530 predicted CDS, 7 ribosomal opero...

Flow structure through pool-riffle sequences and a conceptual model for their sustainability in gravel-bed rivers

Treesearch

D. Caamano; P. Goodwin; J. M. Buffington

2010-01-01

Detailed field measurements and simulations of three-dimensional flow structure were used to develop a conceptual model to explain the sustainability of self-formed pool-riffle sequences in gravel-bed rivers. The analysis was conducted at the Red River Wildlife Management Area in Idaho, USA, and enabled characterization of the flow structure through two consecutive...

Peptide de novo sequencing of mixture tandem mass spectra

PubMed Central

Hotta, Stéphanie Yuki Kolbeck; Verano‐Braga, Thiago; Kjeldsen, Frank

2016-01-01

The impact of mixture spectra deconvolution on the performance of four popular de novo sequencing programs was tested using artificially constructed mixture spectra as well as experimental proteomics data. Mixture fragmentation spectra are recognized as a limitation in proteomics because they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co‐isolation and thus prone to false identifications. The deconvolution approach matched complementary b‐, y‐ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co‐isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced peptides. The improvement was in the range of 20–35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight candidate peptide score distribution and high sensitivity to small changes in the mass spectrum introduced by the employed deconvolution method could explain some of the missing peptide identifications. PMID:27329701

Effect of the reflectional symmetry on the coherent hole transport across DNA hairpins

NASA Astrophysics Data System (ADS)

Zarea, Mehdi; Berlin, Yuri; Ratner, Mark A.

2017-03-01

The coherent hole transfer in three types of DNA hairpins containing strands with adenine (A) and guanine (G) nucleobases has been studied. The investigated hairpins involve An+1GGAn, AnGAGAn, or (AG)2nA strands that connect the hole donor and hole acceptor located on opposite ends of hairpins. The positive charge transfer from the photo-excited donor to the acceptor is shown to be slower for An+1GGAn in comparison with AnGAGAn and (AG)2nA sequences. We have revealed that this is due to the reflectional symmetry of the last two sequences with respect to the axis passing through the middle base. As has been demonstrated, the symmetry of the sequence structure manifests itself in the reflectional symmetry of the energy eigenstates. In addition, it has been shown that (AG)2nA is the only symmetric sequence with a zero energy state in the middle of the LUMO tight-binding energy band. Based on our theoretical findings, we predict that the hairpin with this sequence should have the fastest coherent hole transfer rate among the class of base sequences studied.

Mannosyltransferase is required for cell wall biosynthesis, morphology and control of asexual development in Neurospora crassa.

PubMed

Bowman, Shaun M; Piwowar, Amy; Ciocca, Maria; Free, Stephen J

2005-01-01

Two Neurospora mutants with a phenotype that includes a tight colonial growth pattern, an inability to form conidia and an inability to form protoperithecia have been isolated and characterized. The relevant mutations were mapped to the same locus on the sequenced Neurospora genome. The mutations responsible for the mutant phenotype then were identified by examining likely candidate genes from the mutant genomes at the mapped locus with PCR amplification and a sequencing assay. The results demonstrate that a map and sequence strategy is a feasible way to identify mutant genes in Neurospora. The gene responsible for the phenotype is a putative alpha-1,2-mannosyltransferase gene. The mutant cell wall has an altered composition demonstrating that the gene functions in cell wall biosynthesis. The results demonstrate that the mnt-1 gene is required for normal cell wall biosynthesis, morphology and for the regulation of asexual development.

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

Kvon, Evgeny Z.; Kamneva, Olga K.; Melo, Uirá S.

The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. In this paper, we identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologsmore » caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution.« less

EVOLUTION OF THE MASS-METALLICITY RELATIONS IN PASSIVE AND STAR-FORMING GALAXIES FROM SPH-COSMOLOGICAL SIMULATIONS

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

Romeo Velona, A. D.; Gavignaud, I.; Meza, A.

2013-06-20

We present results from SPH-cosmological simulations, including self-consistent modeling of supernova feedback and chemical evolution, of galaxies belonging to two clusters and 12 groups. We reproduce the mass-metallicity (ZM) relation of galaxies classified in two samples according to their star-forming (SF) activity, as parameterized by their specific star formation rate (sSFR), across a redshift range up to z = 2. The overall ZM relation for the composite population evolves according to a redshift-dependent quadratic functional form that is consistent with other empirical estimates, provided that the highest mass bin of the brightest central galaxies is excluded. Its slope shows irrelevantmore » evolution in the passive sample, being steeper in groups than in clusters. However, the subsample of high-mass passive galaxies only is characterized by a steep increase of the slope with redshift, from which it can be inferred that the bulk of the slope evolution of the ZM relation is driven by the more massive passive objects. The scatter of the passive sample is dominated by low-mass galaxies at all redshifts and keeps constant over cosmic times. The mean metallicity is highest in cluster cores and lowest in normal groups, following the same environmental sequence as that previously found in the red sequence building. The ZM relation for the SF sample reveals an increasing scatter with redshift, indicating that it is still being built at early epochs. The SF galaxies make up a tight sequence in the SFR-M{sub *} plane at high redshift, whose scatter increases with time alongside the consolidation of the passive sequence. We also confirm the anti-correlation between sSFR and stellar mass, pointing at a key role of the former in determining the galaxy downsizing, as the most significant means of diagnostics of the star formation efficiency. Likewise, an anti-correlation between sSFR and metallicity can be established for the SF galaxies, while on the contrary more active galaxies in terms of simple SFR are also metal-richer. Finally, the [O/Fe] abundance ratio is presented too: we report a strong increasing evolution with redshift at given mass, especially at z {approx}> 1. The expected increasing trend with mass is recovered when only considering the more massive galaxies. We discuss these results in terms of the mechanisms driving the evolution within the high- and low-mass regimes at different epochs: mergers, feedback-driven outflows, and the intrinsic variation of the star formation efficiency.« less

Revisiting the concept of behavior patterns in animal behavior with an example from food-caching sequences in wolves (Canis lupus), coyotes (Canis latrans), and red foxes (Vulpes vulpes).

PubMed

Gadbois, Simon; Sievert, Olivia; Reeve, Catherine; Harrington, F H; Fentress, J C

2015-01-01

We discuss the history, conceptualization, and relevance of behavior patterns in modern ethology by explaining the evolution of the concepts of fixed action patterns and modal action patterns. We present the movement toward a more flexible concept of natural action sequences with significant degrees of (production and expressive) freedom. An example is presented with the food caching behavior of three Canidae species: red fox (Vulpes vulpes), coyote (Canis latrans) and gray wolf (Canis lupus). Evolutionary, ecological, and neuroecological/neuroethological arguments are presented to explain the difference in levels of complexity and stereotypy between Canis and Vulpes. This article is part of a Special Issue entitled: Canine Behavior. Copyright © 2014 Elsevier B.V. All rights reserved.

De novo genome assembly of the red silk cotton tree (Bombax ceiba).

PubMed

Gao, Yong; Wang, Haibo; Liu, Chao; Chu, Honglong; Dai, Dongqin; Song, Shengnan; Yu, Long; Han, Lihong; Fu, Yi; Tian, Bin; Tang, Lizhou

2018-05-01

Bombax ceiba L. (the red silk cotton tree) is a large deciduous tree that is distributed in tropical and sub-tropical Asia as well as northern Australia. It has great economic and ecological importance, with several applications in industry and traditional medicine in many Asian countries. To facilitate further utilization of this plant resource, we present here the draft genome sequence for B. ceiba. We assembled a relatively intact genome of B. ceiba by using PacBio single-molecule sequencing and BioNano optical mapping technologies. The final draft genome is approximately 895 Mb long, with contig and scaffold N50 sizes of 1.0 Mb and 2.06 Mb, respectively. The high-quality draft genome assembly of B. ceiba will be a valuable resource enabling further genetic improvement and more effective use of this tree species.

Spectroscopic Confirmation of Two Massive Red-sequence-selected Galaxy Clusters at Z Approximately Equal to 1.2 in the Sparcs-North Cluster Survey

NASA Technical Reports Server (NTRS)

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

The lowest-metallicity type II supernova from the highest-mass red supergiant progenitor

NASA Astrophysics Data System (ADS)

Anderson, J. P.; Dessart, L.; Gutiérrez, C. P.; Krühler, T.; Galbany, L.; Jerkstrand, A.; Smartt, S. J.; Contreras, C.; Morrell, N.; Phillips, M. M.; Stritzinger, M. D.; Hsiao, E. Y.; González-Gaitán, S.; Agliozzo, C.; Castellón, S.; Chambers, K. C.; Chen, T.-W.; Flewelling, H.; Gonzalez, C.; Hosseinzadeh, G.; Huber, M.; Fraser, M.; Inserra, C.; Kankare, E.; Mattila, S.; Magnier, E.; Maguire, K.; Lowe, T. B.; Sollerman, J.; Sullivan, M.; Young, D. R.; Valenti, S.

2018-05-01

Red supergiants have been confirmed as the progenitor stars of the majority of hydrogen-rich type II supernovae1. However, while such stars are observed with masses >25 M⊙ (ref. 2), detections of >18 M⊙ progenitors remain elusive1. Red supergiants are also expected to form at all metallicities, but discoveries of explosions from low-metallicity progenitors are scarce. Here, we report observations of the type II supernova, SN 2015bs, for which we infer a progenitor metallicity of ≤0.1 Z⊙ from comparison to photospheric-phase spectral models3, and a zero-age main-sequence mass of 17–25 M⊙ through comparison to nebular-phase spectral models4,5. SN 2015bs displays a normal ‘plateau’ light-curve morphology, and typical spectral properties, implying a red supergiant progenitor. This is the first example of such a high-mass progenitor for a ‘normal’ type II supernova, suggesting a link between high-mass red supergiant explosions and low-metallicity progenitors.

Isolation and identification of lactic acid bacteria from fermented red dragon fruit juices.

PubMed

Ong, Yien Yien; Tan, Wen Siang; Rosfarizan, Mohamad; Chan, Eng Seng; Tey, Beng Ti

2012-10-01

Red dragon fruit or red pitaya is rich in potassium, fiber, and antioxidants. Its nutritional properties and unique flesh color have made it an attractive raw material of various types of food products and beverages including fermented beverages or enzyme drinks. In this study, phenotypic and genotypic methods were used to confirm the identity of lactic acid bacteria (LAB) appeared in fermented red dragon fruit (Hylocereus polyrhizus) beverages. A total of 21 isolates of LAB were isolated and characterized. They belonged to the genus of Enterococcus based on their biochemical characteristics. The isolates can be clustered into two groups by using the randomly amplified polymorphic DNA method. Nucleotide sequencing and restriction fragment length polymorphism of the 16S rRNA region suggested that they were either Enterococcus faecalis or Enterococcus durans. Current research revealed the use of biochemical analyses and molecular approaches to identify the microbial population particularly lactic acid bacteria from fermented red dragon fruit juices. © 2012 Institute of Food Technologists®

Contrasting molecular and morphological evidence for the identification of an anomalous Buteo: a cautionary tale for hybrid diagnosis

PubMed Central

2017-01-01

An adult Buteo was found dead as a road-kill south of Sacramento, California, and was thought to represent the first state record of the eastern Red-shouldered Hawk (B. lineatus lineatus;). It is now a specimen in the Museum of Wildlife and Fisheries Biology (WFB 4816) at the University of California, Davis. We examined this specimen and found that many of its plumage characters differed from all other adult Red-shouldered Hawks examined, including nominate adults. Plumage markings and measurements were intermediate between Red-tailed Hawk (Buteo jamaicensis, ssp calurus) and Red-shouldered Hawk (ssp elegans), leading us to hypothesize that the bird was a hybrid. However, mtDNA sequences and nuDNA microsatellites proved definitively that the bird was a Red-shouldered Hawk, most likely of eastern origin. This case illustrates that apparent hybrids or apparent vagrants could be individuals with anomalous phenotypes caused by rare genetic variation or novel epigenetic effects. PMID:28097061

Differential global gene expression in red and white skeletal muscle

NASA Technical Reports Server (NTRS)

Campbell, W. G.; Gordon, S. E.; Carlson, C. J.; Pattison, J. S.; Hamilton, M. T.; Booth, F. W.

2001-01-01

The differences in gene expression among the fiber types of skeletal muscle have long fascinated scientists, but for the most part, previous experiments have only reported differences of one or two genes at a time. The evolving technology of global mRNA expression analysis was employed to determine the potential differential expression of approximately 3,000 mRNAs between the white quad (white muscle) and the red soleus muscle (mixed red muscle) of female ICR mice (30-35 g). Microarray analysis identified 49 mRNA sequences that were differentially expressed between white and mixed red skeletal muscle, including newly identified differential expressions between muscle types. For example, the current findings increase the number of known, differentially expressed mRNAs for transcription factors/coregulators by nine and signaling proteins by three. The expanding knowledge of the diversity of mRNA expression between white and mixed red muscle suggests that there could be quite a complex regulation of phenotype between muscles of different fiber types.

Formation of the black-hole binary M33 X-7 through mass exchange in a tight massive system.

PubMed

Valsecchi, Francesca; Glebbeek, Evert; Farr, Will M; Fragos, Tassos; Willems, Bart; Orosz, Jerome A; Liu, Jifeng; Kalogera, Vassiliki

2010-11-04

The X-ray source M33 X-7 in the nearby galaxy Messier 33 is among the most massive X-ray binary stellar systems known, hosting a rapidly spinning, 15.65M(⊙) black hole orbiting an underluminous, 70M(⊙) main-sequence companion in a slightly eccentric 3.45-day orbit (M(⊙), solar mass). Although post-main-sequence mass transfer explains the masses and tight orbit, it leaves unexplained the observed X-ray luminosity, the star's underluminosity, the black hole's spin and the orbital eccentricity. A common envelope phase, or rotational mixing, could explain the orbit, but the former would lead to a merger and the latter to an overluminous companion. A merger would also ensue if mass transfer to the black hole were invoked for its spin-up. Here we report simulations of evolutionary tracks which reveal that if M33 X-7 started as a primary body of 85M(⊙)-99M(⊙) and a secondary body of 28M(⊙)-32M(⊙), in a 2.8-3.1-d orbit, its observed properties can be consistently explained. In this model, the main-sequence primary transfers part of its envelope to the secondary and loses the rest in a wind; it ends its life as a ∼16M(⊙) helium star with an iron-nickel core that collapses to a black hole (with or without an accompanying supernova). The release of binding energy, and possibly collapse asymmetries, 'kick' the nascent black hole into an eccentric orbit. Wind accretion explains the X-ray luminosity, and the black-hole spin can be natal.

Identification and characterization of a DnaJ gene from red alga Pyropia yezoensis (Bangiales, Rhodophyta)

NASA Astrophysics Data System (ADS)

Liu, Jiao; Li, Xianchao; Tang, Xuexi; Zhou, Bin

2016-03-01

Members of the DnaJ family are proteins that play a pivotal role in various cellular processes, such as protein folding, protein transport and cellular responses to stress. In the present study, we identified and characterized the full-length DnaJ cDNA sequence from expressed sequence tags of Pyropia yezoensis ( PyDnaJ) via rapid identification of cDNA ends. This cDNA encoded a protein of 429 amino acids, which shared high sequence similarity with other identified DnaJ proteins, such as a heat shock protein 40/DnaJ from Pyropia haitanensis. The relative mRNA expression level of PyDnaJ was investigated using real-time PCR to determine its specific expression during the algal life cycle and during desiccation. The relative mRNA expression level in sporophytes was higher than that in gametophytes and significantly increased during the whole desiccation process. These results indicate that PyDnaJ is an authentic member of the DnaJ family in plants and red algae and might play a pivotal role in mitigating damage to P. yezoensis during desiccation.

Multistage crack seal vein and hydrothermal Ni enrichment in serpentinized ultramafic rocks (Koniambo massif, New Caledonia)

NASA Astrophysics Data System (ADS)

Cathelineau, Michel; Myagkiy, Andrey; Quesnel, Benoit; Boiron, Marie-Christine; Gautier, Pierre; Boulvais, Philippe; Ulrich, Marc; Truche, Laurent; Golfier, Fabrice; Drouillet, Maxime

2017-10-01

Sets of fractures and breccia sealed by Ni-rich silicates and quartz occur within saprock of the New Caledonian regolith developed over ultramafic rocks. The crystallization sequence in fractures is as follows: (1) serpentine stage: lizardite > polygonal serpentine > white lizardite; (2) Ni stage: Ni-Mg kerolite followed by red-brown microcrystalline quartz; and (3) supergene stages. The red-brown microcrystalline quartz corresponds to the very last stage of the Ni sequence and is inferred to have precipitated within the 50-95 °C temperature range. It constitutes also the main cement of breccia that has all the typical features of hydraulic fracturing. The whole sequence is therefore interpreted as the result of hydrothermal fluid circulation under medium to low temperature and fluctuating fluid pressure. Although frequently described as the result of a single downward redistribution of Ni and Mg leached in the upper part of the regolith under ambient temperature, the Ni silicate veins thus appear as the result of recurrent crack and seal process, corresponding to upward medium temperature fluid convection, hydraulic fracturing and subsequent fluid mixing, and mineral deposition.

The Missing Link: Early Methane ("T") Dwarfs in the Sloan Digital Sky Survey.

PubMed

Leggett; Geballe; Fan; Schneider; Gunn; Lupton; Knapp; Strauss; McDaniel; Golimowski; Henry; Peng; Tsvetanov; Uomoto; Zheng; Hill; Ramsey; Anderson; Annis; Bahcall; Brinkmann; Chen; Csabai; Fukugita; Hennessy; Hindsley; Ivezic; Lamb; Munn; Pier; Schlegel; Smith; Stoughton; Thakar; York

2000-06-10

We report the discovery of three cool brown dwarfs that fall in the effective temperature gap between the latest L dwarfs currently known, with no methane absorption bands in the 1-2.5 µm range, and the previously known methane (T) dwarfs, whose spectra are dominated by methane and water. The newly discovered objects were detected as very red objects in the Sloan Digital Sky Survey imaging data and have JHK colors between the red L dwarfs and the blue Gl 229B-like T dwarfs. They show both CO and CH(4) absorption in their near-infrared spectra in addition to H(2)O, with weaker CH(4) absorption features in the H and K bands than those in all other methane dwarfs reported to date. Due to the presence of CH(4) in these bands, we propose that these objects are early T dwarfs. The three form part of the brown dwarf spectral sequence and fill in the large gap in the overall spectral sequence from the hottest main-sequence stars to the coolest methane dwarfs currently known.

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence.

PubMed

Meuleman, Wouter; Peric-Hupkes, Daan; Kind, Jop; Beaudry, Jean-Bernard; Pagie, Ludo; Kellis, Manolis; Reinders, Marcel; Wessels, Lodewyk; van Steensel, Bas

2013-02-01

In metazoans, the nuclear lamina is thought to play an important role in the spatial organization of interphase chromosomes, by providing anchoring sites for large genomic segments named lamina-associated domains (LADs). Some of these LADs are cell-type specific, while many others appear constitutively associated with the lamina. Constitutive LADs (cLADs) may contribute to a basal chromosome architecture. By comparison of mouse and human lamina interaction maps, we find that the sizes and genomic positions of cLADs are strongly conserved. Moreover, cLADs are depleted of synteny breakpoints, pointing to evolutionary selective pressure to keep cLADs intact. Paradoxically, the overall sequence conservation is low for cLADs. Instead, cLADs are universally characterized by long stretches of DNA of high A/T content. Cell-type specific LADs also tend to adhere to this "A/T rule" in embryonic stem cells, but not in differentiated cells. This suggests that the A/T rule represents a default positioning mechanism that is locally overruled during lineage commitment. Analysis of paralogs suggests that during evolution changes in A/T content have driven the relocation of genes to and from the nuclear lamina, in tight association with changes in expression level. Taken together, these results reveal that the spatial organization of mammalian genomes is highly conserved and tightly linked to local nucleotide composition.

Occludin confers adhesiveness when expressed in fibroblasts.

PubMed

Van Itallie, C M; Anderson, J M

1997-05-01

Occludin is an integral membrane protein specifically associated with tight junctions. Previous studies suggest it is likely to function in forming the intercellular seal. In the present study, we expressed occludin under an inducible promotor in occludin-null fibroblasts to determine whether this protein confers intercellular adhesion. When human occludin is stably expressed in NRK and Rat-1 fibroblasts, which lack endogenous occludin and tight junctions but do have well developed ZO-1-containing adherens-like junctions, occludin colocalizes with ZO-1 to points of cell-cell contact. In contrast, L-cell fibroblasts which lack cadherin-based adherens junctions, target neither ZO-1 nor occludin to sites of cell contact. Occludin-induced adhesion was next quantified using a suspended cell assay. In NRK and Rat-1 cells, occludin expression induces adhesion in the absence of calcium, thus independent of cadherin-cadherin contacts. In contrast, L-cells are nonadhesive in this assay and show no increase in adhesion after induction of occludin expression. Binding of an antibody to the first of the putative extracellular loops of occludin confirmed that this sequence was exposed on the cell surface, and synthetic peptides containing the amino acid sequence of this loop inhibit adhesion induced by occludin expression. These results suggest that the extracellular surface of occludin is directly involved in cell-cell adhesion and the ability to confer adhesiveness correlates with the ability to colocalize with its cytoplasmic binding protein, ZO-1.

Theory of prokaryotic genome evolution.

PubMed

Sela, Itamar; Wolf, Yuri I; Koonin, Eugene V

2016-10-11

Bacteria and archaea typically possess small genomes that are tightly packed with protein-coding genes. The compactness of prokaryotic genomes is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. Here, by fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. These results suggest that the number of genes in prokaryotic genomes reflects the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias (i.e., the rate of deletion of genetic material being slightly greater than the rate of acquisition). Thus, new genes acquired by microbial genomes, on average, appear to be adaptive. The tight spacing of protein-coding genes likely results from a combination of the deletion bias and purifying selection that efficiently eliminates nonfunctional, noncoding sequences.

The EspF N-Terminal of Enterohemorrhagic Escherichia coli O157:H7 EDL933w Imparts Stronger Toxicity Effects on HT-29 Cells than the C-Terminal.

PubMed

Wang, Xiangyu; Du, Yanli; Hua, Ying; Fu, Muqing; Niu, Cong; Zhang, Bao; Zhao, Wei; Zhang, Qiwei; Wan, Chengsong

2017-01-01

Enterohemorrhagic Escherichia coli (EHEC) O157:H7 EspF is an important multifunctional protein that destroys the tight junctions of intestinal epithelial cells and promotes host cell apoptosis. However, its molecular mechanism remains elusive. We knocked out the espF sequence (747 bp, Δ espF ), N-terminal sequence (219 bp, Δ espF N ), and C-terminal sequence (528 bp, Δ espF C ) separately using the pKD46-mediated λ Red homologous recombination system. Then, we built the corresponding complementation strains, namely, Δ espF/pespF , Δ espF N /pespF N , and Δ espF C /pespF C by overlap PCR, which were used in infecting HT-29 cells and BALB/C mice. The level of reactive oxygen species, cell apoptosis, mitochondrial trans-membrane potential, inflammatory factors, transepithelial electrical resistance (TER), and animal mortality were evaluated by DCFH-DA, double staining of Annexin V-FITC/PI, JC-1 staining, ELISA kit, and a mouse assay. The wild-type (WT), Δ espF , Δ espF/pespF , Δ espF C , Δ espF C /pespF C , Δ espF N , and Δ espF N /pespF N groups exhibited apoptotic rates of 68.3, 27.9, 64.9, 65.7, 73.4, 41.3, and 35.3% respectively, and mean TNF-α expression levels of 428 pg/mL, 342, 466, 446, 381, 383, and 374 pg/mL, respectively. In addition, the apoptotic rates and TNF-α levels of the WT, Δ espF/pespF , and Δ espF C were significantly higher than that of Δ espF , Δ espF N , Δ espF C /pespF C , and Δ espF N /pespF N group ( p < 0.05). The N-terminal of EspF resulted in an increase in the number of apoptotic cells, TNF-α secretion, ROS generation, mitochondria apoptosis, and pathogenicity in BalB/c mice. In conclusion, the N-terminal domain of the Enterohemorrhagic E. coli O157:H7 EspF more strongly promotes apoptosis and inflammation than the C-terminal domain.

Bionanomaterials and Bioinspired Nanostructures for Selective Vapor Sensing

DTIC Science & Technology

2013-04-03

with the current baseline shown with yellow points. DNA sequence: 5′ GAG TCT GTG GAG GAG GTA GTC 3′. Green and black arrows in panels a–c show the...SWCNT transducer to TNT (red circles), RDX ( gray triangles), and HPT (black squares). Blue arrows in panels b and c show introduction of analyte vapors...increasing partial pressure ranging from 0 to 0.07 P/P0. Vapor concentrations are 0 ( gray dashed lines), 0.02 (red curves), 0.04 ( gold curves), and 0.07

Remote image analysis for Mars Exploration Rover mobility and manipulation operations

NASA Technical Reports Server (NTRS)

Leger, Chris; Deen, Robert G.; Bonitz, Robert G.

2005-01-01

NASA's Mars Exploration Rovers are two sixwheeled, 175-kg robotic vehicles which have operated on Mars for over a year as of March 2005. The rovers are controlled by teams who must understand the rover's surroundings and develop command sequences on a daily basis. The tight tactical planning timeline and everchanging environment call for tools that allow quick assessment of potential manipulator targets and traverse goals, since command sequences must be developed in a matter of hours after receipt of new data from the rovers. Reachability maps give a visual indication of which targets are reachable by each rover's manipulator, while slope and solar energy maps show the rover operator which terrain areas are safe and unsafe from different standpoints.

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

Kim, Suk; Rey, Soo-Chang; Lisker, Thorsten

We present ultraviolet (UV) color-magnitude relations (CMRs) of early-type dwarf galaxies in the Virgo cluster, based on Galaxy Evolution Explorer (GALEX) UV and Sloan Digital Sky Survey (SDSS) optical imaging data. We find that dwarf lenticular galaxies (dS0s), including peculiar dwarf elliptical galaxies (dEs) with disk substructures and blue centers, show a surprisingly distinct and tight locus separated from that of ordinary dEs, which is not clearly seen in previous CMRs. The dS0s in UV CMRs follow a steeper sequence than dEs and show bluer UV-optical color at a given magnitude. We also find that the UV CMRs of dEsmore » in the outer cluster region are slightly steeper than that of their counterparts in the inner region, due to the existence of faint, blue dEs in the outer region. We explore the observed CMRs with population models of a luminosity-dependent delayed exponential star formation history. We confirm that the feature of delayed star formation of early-type dwarf galaxies in the Virgo cluster is strongly correlated with their morphology and environment. The observed CMR of dS0s is well matched by models with relatively long delayed star formation. Our results suggest that dS0s are most likely transitional objects at the stage of subsequent transformation of late-type progenitors to ordinary red dEs in the cluster environment. In any case, UV photometry provides a powerful tool to disentangle the diverse subpopulations of early-type dwarf galaxies and uncover their evolutionary histories.« less

Timing the formation and assembly of early-type galaxies via spatially resolved stellar populations analysis

NASA Astrophysics Data System (ADS)

Martín-Navarro, Ignacio; Vazdekis, Alexandre; Falcón-Barroso, Jesús; La Barbera, Francesco; Yıldırım, Akın; van de Ven, Glenn

2018-04-01

To investigate star formation and assembly processes of massive galaxies, we present here a spatially resolved stellar population analysis of a sample of 45 elliptical galaxies (Es) selected from the Calar Alto Legacy Integral Field Area survey. We find rather flat age and [Mg/Fe] radial gradients, weakly dependent on the effective velocity dispersion of the galaxy within half-light radius. However, our analysis shows that metallicity gradients become steeper with increasing galaxy velocity dispersion. In addition, we have homogeneously compared the stellar population gradients of our sample of Es to a sample of nearby relic galaxies, i.e. local remnants of the high-z population of red nuggets. This comparison indicates that, first, the cores of present-day massive galaxies were likely formed in gas-rich, rapid star formation events at high redshift (z ≳ 2). This led to radial metallicity variations steeper than observed in the local Universe, and positive [Mg/Fe] gradients. Secondly, our analysis also suggests that a later sequence of minor dry mergers, populating the outskirts of early-type galaxies (ETGs), flattened the pristine [Mg/Fe] and metallicity gradients. Finally, we find a tight age-[Mg/Fe] relation, supporting that the duration of the star formation is the main driver of the [Mg/Fe] enhancement in massive ETGs. However, the star formation time-scale alone is not able to fully explain our [Mg/Fe] measurements. Interestingly, our results match the expected effect that a variable stellar initial mass function would have on the [Mg/Fe] ratio.

WEAK LENSING MEASUREMENT OF GALAXY CLUSTERS IN THE CFHTLS-WIDE SURVEY

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

Shan Huanyuan; Tao Charling; Kneib, Jean-Paul

2012-03-20

We present the first weak gravitational lensing analysis of the completed Canada-France-Hawaii Telescope Legacy Survey (CFHTLS). We study the 64 deg{sup 2} W1 field, the largest of the CFHTLS-Wide survey fields, and present the largest contiguous weak lensing convergence 'mass map' yet made. 2.66 million galaxy shapes are measured, using the Kaiser Squires and Broadhurst Method (KSB) pipeline verified against high-resolution Hubble Space Telescope imaging that covers part of the CFHTLS. Our i'-band measurements are also consistent with an analysis of independent r'-band imaging. The reconstructed lensing convergence map contains 301 peaks with signal-to-noise ratio {nu} > 3.5, consistent withmore » predictions of a {Lambda}CDM model. Of these peaks, 126 lie within 3.'0 of a brightest central galaxy identified from multicolor optical imaging in an independent, red sequence survey. We also identify seven counterparts for massive clusters previously seen in X-ray emission within 6 deg{sup 2} XMM-LSS survey. With photometric redshift estimates for the source galaxies, we use a tomographic lensing method to fit the redshift and mass of each convergence peak. Matching these to the optical observations, we confirm 85 groups/clusters with {chi}{sup 2}{sub reduced} < 3.0, at a mean redshift (z{sub c} ) = 0.36 and velocity dispersion ({sigma}{sub c}) = 658.8 km s{sup -1}. Future surveys, such as DES, LSST, KDUST, and EUCLID, will be able to apply these techniques to map clusters in much larger volumes and thus tightly constrain cosmological models.« less

Water input requirements of the rapidly shrinking Dead Sea

NASA Astrophysics Data System (ADS)

Abu Ghazleh, Shahrazad; Hartmann, Jens; Jansen, Nils; Kempe, Stephan

2009-05-01

The deepest point on Earth, the Dead Sea level, has been dropping alarmingly since 1978 by 0.7 m/a on average due to the accelerating water consumption in the Jordan catchment and stood in 2008 at 420 m below sea level. In this study, a terrain model of the surface area and water volume of the Dead Sea was developed from the Shuttle Radar Topography Mission data using ArcGIS. The model shows that the lake shrinks on average by 4 km2/a in area and by 0.47 km3/a in volume, amounting to a cumulative loss of 14 km3 in the last 30 years. The receding level leaves almost annually erosional terraces, recorded here for the first time by Differential Global Positioning System field surveys. The terrace altitudes were correlated among the different profiles and dated to specific years of the lake level regression, illustrating the tight correlation between the morphology of the terrace sequence and the receding lake level. Our volume-level model described here and previous work on groundwater inflow suggest that the projected Dead Sea-Red Sea channel or the Mediterranean-Dead Sea channel must have a carrying capacity of >0.9 km3/a in order to slowly re-fill the lake to its former level and to create a sustainable system of electricity generation and freshwater production by desalinization. Moreover, such a channel will maintain tourism and potash industry on both sides of the Dead Sea and reduce the natural hazard caused by the recession.

Cerebral malaria in mice: demonstration of cytoadherence of infected red blood cells and microrheologic correlates.

PubMed

Kaul, D K; Nagel, R L; Llena, J F; Shear, H L

1994-04-01

To understand the microcirculatory events during cerebral malaria, we have studied the lethal strain of rodent Plasmodia, Plasmodium yoelii 17XL, originally described by Yoeli and Hargreaves in 1974. The virulence of P. yoelii 17XL is caused by intravascular sequestration of infected red blood cells (IRBCs), especially in the brain vessels and capillaries. This mouse model resembles human P. falciparum infection more closely than P. berghei ANKA infection since it shows little, if any, inflammation of the brain. In vivo microcirculatory studies on cytoadherence of IRBCs were performed using the cremaster muscle preparation, which is an easily accessible vasculature for intravital observations. Ex vivo assay of cytoadherence was carried out in the artificially perfused mesocecum preparation of the rat. The results in either preparation demonstrated cytoadherence of IRBCs that was restricted to postcapillary venules. Furthermore, the in vivo measurements showed the prevalence of cytoadherence in small-diameter (< 40 microns) venules in accordance with the local wall shear rates. The parasitized animals demonstrated significantly reduced red blood cell velocities and wall shear rates in the small-diameter postcapillary venules of the cremaster. The relationship between cytoadherence and venular wall shear rates was also reflected in the inverse correlation between the number of adhered cells and the venular diameter in the ex vivo mesocecum preparation. In the ex vivo preparation, cytoadherence of IRBCs was accompanied by a higher peripheral resistance. Transmission electron microscopy of the cremaster muscle and brain tissues showed a tight association of IRBCs with the endothelium of small venules. These observations demonstrate that cytoadherence of P. yoelii 17XL-infected mouse red blood cells is very similar to that of P. falciparum-infected cells. Thus, this model should allow a detailed analysis of the molecular mechanisms involved in the generation of cerebral malaria by cytoadherence of the infected red blood cells to the vascular endothelium.

Occurrence of Giardia in Swedish Red Foxes ( Vulpes vulpes ).

PubMed

Debenham, John J; Landuyt, Hanne; Troell, Karin; Tysnes, Kristoffer; Robertson, Lucy J

2017-07-01

Giardia duodenalis is an intestinal protozoan capable of causing gastrointestinal disease in a range of vertebrate hosts. It is transmitted via the fecal-oral route. Understanding the epidemiology of G. duodenalis in animals is important, both for public health and for the health of the animals it infects. We investigated the occurrence of G. duodenalis in wild Swedish red foxes ( Vulpes vulpes ), with the aim of providing preliminary information on how this abundant predator might be involved in the transmission and epidemiology of G. duodenalis . Fecal samples (n=104) were analysed for G. duodenalis using a commercially available direct immunofluorescent antibody test. Giardia duodenalis cysts were found in 44% (46/104) of samples, with foxes excreting 100 to 140,500 cysts per gram of feces (mean, 4,930; median, 600). Molecular analysis, using PCR with sequencing of PCR amplicons, was performed on 14 samples, all containing over 2,000 cysts per gram feces. Amplification only occurred in four samples at the tpi gene, sequencing of which revealed assemblage B in all four samples. This study provides baseline information on the role of red foxes in the transmission dynamics of G. duodenalis in Sweden.

RNA-seq analysis of the transcriptional response to blue and red light in the extremophilic red alga, Cyanidioschyzon merolae.

PubMed

Tardu, Mehmet; Dikbas, Ugur Meric; Baris, Ibrahim; Kavakli, Ibrahim Halil

2016-11-01

Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red lights were found to regulate 35 % of the total genes in C. merolae. Blue light affected the transcription of genes involved in protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae.

RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters

PubMed Central

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. PMID:26930599

Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution.

PubMed

Yarbrough, D; Wachter, R M; Kallio, K; Matz, M V; Remington, S J

2001-01-16

The crystal structure of DsRed, a red fluorescent protein from a corallimorpharian, has been determined at 2.0-A resolution by multiple-wavelength anomalous dispersion and crystallographic refinement. Crystals of the selenomethionine-substituted protein have space group P2(1) and contain a tetramer with 222 noncrystallographic symmetry in the asymmetric unit. The refined model has satisfactory stereochemistry and a final crystallographic R factor of 0.162. The protein, which forms an obligatory tetramer in solution and in the crystal, is a squat rectangular prism comprising four protomers whose fold is extremely similar to that of the Aequorea victoria green fluorescent protein despite low ( approximately 23%) amino acid sequence homology. The monomer consists of an 11-stranded beta barrel with a coaxial helix. The chromophores, formed from the primary sequence -Gln-Tyr-Gly- (residues 66-68), are arranged in a approximately 27 x 34-A rectangular array in two approximately antiparallel pairs. The geometry at the alpha carbon of Gln-66 (refined without stereochemical restraints) is consistent with an sp(2) hybridized center, in accord with the proposal that red fluorescence is because of an additional oxidation step that forms an acylimine extension to the chromophore [Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K. & Tsien, R. Y. (2000) Proc. Natl. Acad. Sci. USA 87, 11990-11995]. The carbonyl oxygen of Phe-65 is almost 90 degrees out of the plane of the chromophore, consistent with theoretical calculations suggesting that this is the minimum energy conformation of this moiety despite the conjugation of this group with the rest of the chromophore.

De Novo Assembly and Comparative Transcriptome Analyses of Red and Green Morphs of Sweet Basil Grown in Full Sunlight

PubMed Central

Torre, Sara; Tattini, Massimiliano; Brunetti, Cecilia; Guidi, Lucia; Gori, Antonella; Marzano, Cristina; Landi, Marco; Sebastiani, Federico

2016-01-01

Sweet basil (Ocimum basilicum), one of the most popular cultivated herbs worldwide, displays a number of varieties differing in several characteristics, such as the color of the leaves. The development of a reference transcriptome for sweet basil, and the analysis of differentially expressed genes in acyanic and cyanic cultivars exposed to natural sunlight irradiance, has interest from horticultural and biological point of views. There is still great uncertainty about the significance of anthocyanins in photoprotection, and how green and red morphs may perform when exposed to photo-inhibitory light, a condition plants face on daily and seasonal basis. We sequenced the leaf transcriptome of the green-leaved Tigullio (TIG) and the purple-leaved Red Rubin (RR) exposed to full sunlight over a four-week experimental period. We assembled and annotated 111,007 transcripts. A total of 5,468 and 5,969 potential SSRs were identified in TIG and RR, respectively, out of which 66 were polymorphic in silico. Comparative analysis of the two transcriptomes showed 2,372 differentially expressed genes (DEGs) clustered in 222 enriched Gene ontology terms. Green and red basil mostly differed for transcripts abundance of genes involved in secondary metabolism. While the biosynthesis of waxes was up-regulated in red basil, the biosynthesis of flavonols and carotenoids was up-regulated in green basil. Data from our study provides a comprehensive transcriptome survey, gene sequence resources and microsatellites that can be used for further investigations in sweet basil. The analysis of DEGs and their functional classification also offers new insights on the functional role of anthocyanins in photoprotection. PMID:27483170

Neglected intravascular pathogens, Babesia vulpes and haemotropic Mycoplasma spp. in European red fox (Vulpes vulpes) population.

PubMed

Koneval, Martina; Miterpáková, Martina; Hurníková, Zuzana; Blaňarová, Lucia; Víchová, Bronislava

2017-08-30

Wild animals, especially canids, are important reservoirs of vector-borne pathogens, that are transmitted by the ticks and other bloodsucking arthropods. In total, 300 red foxes (Vulpes vulpes), shot by the hunters in eastern and northern Slovakia, were screened for the presence of vector-borne pathogens by PCR-based methods Blood samples were obtained from nine red foxes and tissue samples originated from 291 animals (the liver tissue samples from 49 foxes and spleen samples from 242 red foxes). Babesia vulpes and haemotropic Mycoplasma species were identified by amplification and sequencing of 18S rRNA and 16S rRNA gene fragments, respectively. Overall, the presence of these pathogens was recorded in 12.3% of screened DNA samples. Altogether 9.7% (29/300) of investigated foxes carried DNA of Babesia spp. In total, 12 out of 29 Babesia spp. PCR - positive amplicons were further sequenced and identified as B. vulpes (41.4%; 12/29), remaining 17 samples are referred as Babesia sp. (58.6%; 17/29). Overall prevalence of B. vulpes reached 4.0% (n=300). Thirteen (4.3%) samples tested positive for distinct Mycoplasma species. To the best of our knowledge, this study brings the first information on B. vulpes infection in red foxes in Slovakia, and the first data on the prevalence and diversity of haemotropic Mycoplasma spp. in European red fox population. Moreover, co-infections with B. vulpes and Mycoplasma spp. were confirmed in 1.7% of tested DNA samples. The relatively high rates of blood pathogen' prevalence and species diversity in wild foxes indicate the role of the fox population in the maintenance of the parasites in sylvatic cycles and strengthen the assumption that foxes play an important role in spreading of infectious microorganisms within and outside the natural foci. Copyright © 2017 Elsevier B.V. All rights reserved.

GREEN GALAXIES IN THE COSMOS FIELD

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

Pan, Zhizheng; Kong, Xu; Fan, Lulu, E-mail: panzz@mail.ustc.edu.cn, E-mail: xkong@ustc.edu.cn

2013-10-10

We present research on the morphologies, spectra, and environments of ≈2350 'green valley' galaxies at 0.2 < z < 1.0 in the COSMOS field. The bimodality of dust-corrected NUV–r {sup +} color is used to define 'green valley'; it removes dusty star-forming galaxies from galaxies that are truly transitioning between the blue cloud and the red sequence. Morphological parameters of green galaxies are intermediate between those of blue and red galaxy populations, both on the Gini-asymmetry and the Gini-M{sub 20} planes. Approximately 60%-70% of green disk galaxies have intermediate or big bulges, and only 5%-10% are pure disk systems, basedmore » on morphological classification using the Zurich Estimator of Structural Types. The obtained average spectra of green galaxies are intermediate between blue and red ones in terms of [O II], Hα, and Hβ emission lines. Stellar population synthesis on the average spectra shows that green galaxies are on average older than blue galaxies but younger than red galaxies. Green galaxies and blue galaxies have similar projected galaxy density (Σ{sub 10}) distributions at z > 0.7. At z < 0.7, the fractions of M{sub *} < 10{sup 10.0} M{sub ☉} green galaxies located in a dense environment are found to be significantly larger than those of blue galaxies. The morphological and spectral properties of green galaxies are consistent with the transitioning population between the blue cloud and the red sequence. The possible mechanisms for quenching star formation activities in green galaxies are discussed. The importance of active galactic nucleus feedback cannot be well constrained in our study. Finally, our findings suggest that environmental conditions, most likely starvation and harassment, significantly affect the transformation of M{sub *} < 10{sup 10.0} M{sub ☉} blue galaxies into red galaxies, especially at z < 0.5.« less

Comparison of Microbiomes between Red Poultry Mite Populations (Dermanyssus gallinae): Predominance of Bartonella-like Bacteria.

PubMed

Hubert, Jan; Erban, Tomas; Kopecky, Jan; Sopko, Bruno; Nesvorna, Marta; Lichovnikova, Martina; Schicht, Sabine; Strube, Christina; Sparagano, Olivier

2017-11-01

Blood feeding red poultry mites (RPM) serve as vectors of pathogenic bacteria and viruses among vertebrate hosts including wild birds, poultry hens, mammals, and humans. The microbiome of RPM has not yet been studied by high-throughput sequencing. RPM eggs, larvae, and engorged adult/nymph samples obtained in four poultry houses in Czechia were used for microbiome analyses by Illumina amplicon sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. A laboratory RPM population was used as positive control for transcriptome analysis by pyrosequencing with identification of sequences originating from bacteria. The samples of engorged adult/nymph stages had 100-fold more copies of 16S rRNA gene copies than the samples of eggs and larvae. The microbiome composition showed differences among the four poultry houses and among observed developmental stadia. In the adults' microbiome 10 OTUs comprised 90 to 99% of all sequences. Bartonella-like bacteria covered between 30 and 70% of sequences in RPM microbiome and 25% bacterial sequences in transcriptome. The phylogenetic analyses of 16S rRNA gene sequences revealed two distinct groups of Bartonella-like bacteria forming sister groups: (i) symbionts of ants; (ii) Bartonella genus. Cardinium, Wolbachia, and Rickettsiella sp. were found in the microbiomes of all tested stadia, while Spiroplasma eriocheiris and Wolbachia were identified in the laboratory RPM transcriptome. The microbiomes from eggs, larvae, and engorged adults/nymphs differed. Bartonella-like symbionts were found in all stadia and sampling sites. Bartonella-like bacteria was the most diversified group within the RPM microbiome. The presence of identified putative pathogenic bacteria is relevant with respect to human and animal health issues while the identification of symbiontic bacteria can lead to new control methods targeting them to destabilize the arthropod host.

Comprehensive red blood cell and platelet antigen prediction from whole genome sequencing: proof of principle

PubMed Central

Westhoff, Connie M.; Uy, Jon Michael; Aguad, Maria; Smeland‐Wagman, Robin; Kaufman, Richard M.; Rehm, Heidi L.; Green, Robert C.; Silberstein, Leslie E.

2015-01-01

BACKGROUND There are 346 serologically defined red blood cell (RBC) antigens and 33 serologically defined platelet (PLT) antigens, most of which have known genetic changes in 45 RBC or six PLT genes that correlate with antigen expression. Polymorphic sites associated with antigen expression in the primary literature and reference databases are annotated according to nucleotide positions in cDNA. This makes antigen prediction from next‐generation sequencing data challenging, since it uses genomic coordinates. STUDY DESIGN AND METHODS The conventional cDNA reference sequences for all known RBC and PLT genes that correlate with antigen expression were aligned to the human reference genome. The alignments allowed conversion of conventional cDNA nucleotide positions to the corresponding genomic coordinates. RBC and PLT antigen prediction was then performed using the human reference genome and whole genome sequencing (WGS) data with serologic confirmation. RESULTS Some major differences and alignment issues were found when attempting to convert the conventional cDNA to human reference genome sequences for the following genes: ABO, A4GALT, RHD, RHCE, FUT3, ACKR1 (previously DARC), ACHE, FUT2, CR1, GCNT2, and RHAG. However, it was possible to create usable alignments, which facilitated the prediction of all RBC and PLT antigens with a known molecular basis from WGS data. Traditional serologic typing for 18 RBC antigens were in agreement with the WGS‐based antigen predictions, providing proof of principle for this approach. CONCLUSION Detailed mapping of conventional cDNA annotated RBC and PLT alleles can enable accurate prediction of RBC and PLT antigens from whole genomic sequencing data. PMID:26634332

The spectroscopic indistinguishability of red giant branch and red clump stars

NASA Astrophysics Data System (ADS)

Masseron, T.; Hawkins, K.

2017-01-01

Context. Stellar spectroscopy provides useful information on the physical properties of stars such as effective temperature, metallicity and surface gravity. However, those photospheric characteristics are often hampered by systematic uncertainties. The joint spectro-sismo project (APOGEE+Kepler, aka APOKASC) of field red giants has revealed a puzzling offset between the surface gravities (log g) determined spectroscopically and those determined using asteroseismology, which is largely dependent on the stellar evolutionary status. Aims: Therefore, in this letter, we aim to shed light on the spectroscopic source of the offset. Methods: We used the APOKASC sample to analyse the dependencies of the log g discrepancy as a function of stellar mass and stellar evolutionary status. We discuss and study the impact of some neglected abundances on spectral analysis of red giants, such as He and carbon isotopic ratio. Results: We first show that, for stars at the bottom of the red giant branch where the first dredge-up had occurred, the discrepancy between spectroscopic log g and asteroseismic log g depends on stellar mass. This seems to indicate that the log g discrepancy is related to CN cycling. Among the CN-cycled elements, we demonstrate that the carbon isotopic ratio (12C /13C) has the largest impact on stellar spectrum. In parallel, we observe that this log g discrepancy shows a similar trend as the 12C /13C ratios as expected by stellar evolution theory. Although we did not detect a direct spectroscopic signature of 13C, other corroborating evidences suggest that the discrepancy in log g is tightly correlated to the production of 13C in red giants. Moreover, by running the data-driven algorithm (the Cannon) on a synthetic grid trained on the APOGEE data, we try to evaluate more quantitatively the impact of various 12C /13C ratios. Conclusions: While we have demonstrated that 13C indeed impacts all parameters, the size of the impact is smaller than the observed offset in log g. If further tests confirm that 13C is not the main element responsible of the log g problem, the number of spectroscopic effects remaining to be investigated is now relatively limited (if any).

Loop-mediated isothermal amplification (LAMP) assay-A rapid detection tool for identifying red fox (Vulpes vulpes) DNA in the carcasses of harbour porpoises (Phocoena phocoena).

PubMed

Heers, Teresa; van Neer, Abbo; Becker, André; Grilo, Miguel Luca; Siebert, Ursula; Abdulmawjood, Amir

2017-01-01

Carcasses of wild animals are often visited by different scavengers. However, determining which scavenger caused certain types of bite marks is particularly difficult and knowledge thereof is lacking. Therefore, a loop-mediated isothermal amplification (LAMP) assay (target sequence cytochrome b) was developed to detect red fox DNA in carcasses of harbour porpoises. The MSwab™ method for direct testing without prior DNA isolation was validated. As a detection device, the portable real-time fluorometer Genie® II was used, which yields rapid results and can be used in field studies without huge laboratory equipment. In addition to in vitro evaluation and validation, a stranded and scavenged harbour porpoise carcass was successfully examined for red fox DNA residues. The developed LAMP method is a valuable diagnostic tool for confirming presumable red fox bite wounds in harbour porpoises without further DNA isolation steps.

High-speed video capillaroscopy method for imaging and evaluation of moving red blood cells

NASA Astrophysics Data System (ADS)

Gurov, Igor; Volkov, Mikhail; Margaryants, Nikita; Pimenov, Aleksei; Potemkin, Andrey

2018-05-01

The video capillaroscopy system with high image recording rate to resolve moving red blood cells with velocity up to 5 mm/s into a capillary is considered. Proposed procedures of the recorded video sequence processing allow evaluating spatial capillary area, capillary diameter and central line with high accuracy and reliability independently on properties of individual capillary. Two-dimensional inter frame procedure is applied to find lateral shift of neighbor images in the blood flow area with moving red blood cells and to measure directly the blood flow velocity along a capillary central line. The developed method opens new opportunities for biomedical diagnostics, particularly, due to long-time continuous monitoring of red blood cells velocity into capillary. Spatio-temporal representation of capillary blood flow is considered. Experimental results of direct measurement of blood flow velocity into separate capillary as well as capillary net are presented and discussed.

First molecular evidence of Hepatozoon canis infection in red foxes and golden jackals from Hungary.

PubMed

Farkas, Róbert; Solymosi, Norbert; Takács, Nóra; Hornyák, Ákos; Hornok, Sándor; Nachum-Biala, Yaarit; Baneth, Gad

2014-07-02

Recently, Hepatozoon canis infection has been detected among shepherd, hunting and stray dogs in the southern part of Hungary, which is considered to be free of Rhipicephalus sanguineus sensu lato and close to the border with Croatia. The aim of this study was to acquire information on the possibility that red foxes and/or golden jackals could play a role in the appearance and spread of H. canis in Hungary. A conventional PCR was used to amplify a 666 bp long fragment of the Hepatozoon 18S rRNA gene from blood samples collected from 334 foxes shot in 231 locations in 16 counties and 15 golden jackals shot in 9 locations in two southwestern counties close to Croatia. A second PCR assay was performed in some of the samples positive by the first PCR to amplify a larger segment (approximately 1500 bp) of the 18S rRNA gene of Hepatozoon spp. for further phylogenetic analysis. Hepatozoon infection was detected in canids shot in 30 locations and 9 counties. Altogether 26 foxes (8.0%, 95% CI: 5-11%) and 9 jackals (60%, 95% CI: 33-81%) were PCR positive. Hepatozoon canis sequences were obtained from 12 foxes and 7 jackals. DNA sequences from 16 animals were 99-100% similar to H. canis from Croatian foxes or dogs while two of the sequences were 99% similar to an Italian fox. Half (13/26) of the infected red foxes and all golden jackals were shot in the two southwestern counties. This is the first report on molecular evidence of H. canis in red foxes (Vulpes vulpes) and golden jackals (Canis aureus) from Hungary, which is considered free from the tick vector of H. canis, R. sanguineus. Although no R. sanguineus sensu lato had been found on infected or non-infected wild canids, the detection of authochnous canine hepatozoonosis in Hungary might imply that the range of R. sanguineus sensu lato has reached this country.

Comparative Transcriptome Analysis of Genes Involved in Anthocyanin Biosynthesis in the Red and Yellow Fruits of Sweet Cherry (Prunus avium L.)

PubMed Central

Wei, Hairong; Chen, Xin; Zong, Xiaojuan; Shu, Huairui; Gao, Dongsheng; Liu, Qingzhong

2015-01-01

Background Fruit color is one of the most important economic traits of the sweet cherry (Prunus avium L.). The red coloration of sweet cherry fruit is mainly attributed to anthocyanins. However, limited information is available regarding the molecular mechanisms underlying anthocyanin biosynthesis and its regulation in sweet cherry. Methodology/Principal Findings In this study, a reference transcriptome of P. avium L. was sequenced and annotated to identify the transcriptional determinants of fruit color. Normalized cDNA libraries from red and yellow fruits were sequenced using the next-generation Illumina/Solexa sequencing platform and de novo assembly. Over 66 million high-quality reads were assembled into 43,128 unigenes using a combined assembly strategy. Then a total of 22,452 unigenes were compared to public databases using homology searches, and 20,095 of these unigenes were annotated in the Nr protein database. Furthermore, transcriptome differences between the four stages of fruit ripening were analyzed using Illumina digital gene expression (DGE) profiling. Biological pathway analysis revealed that 72 unigenes were involved in anthocyanin biosynthesis. The expression patterns of unigenes encoding phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavanone 3’-hydroxylase (F3’H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS) and UDP glucose: flavonol 3-O-glucosyltransferase (UFGT) during fruit ripening differed between red and yellow fruit. In addition, we identified some transcription factor families (such as MYB, bHLH and WD40) that may control anthocyanin biosynthesis. We confirmed the altered expression levels of eighteen unigenes that encode anthocyanin biosynthetic enzymes and transcription factors using quantitative real-time PCR (qRT-PCR). Conclusions/Significance The obtained sweet cherry transcriptome and DGE profiling data provide comprehensive gene expression information that lends insights into the molecular mechanisms underlying anthocyanin biosynthesis. These results will provide a platform for further functional genomic research on this fruit crop. PMID:25799516

Transcriptomic Analysis of Paeonia delavayi Wild Population Flowers to Identify Differentially Expressed Genes Involved in Purple-Red and Yellow Petal Pigmentation

PubMed Central

Wang, Yan; Li, Kui; Zheng, Baoqiang; Miao, Kun

2015-01-01

Tree peony (Paeonia suffruticosa Andrews) is a very famous traditional ornamental plant in China. P. delavayi is a species endemic to Southwest China that has aroused great interest from researchers as a precious genetic resource for flower color breeding. However, the current understanding of the molecular mechanisms of flower pigmentation in this plant is limited, hindering the genetic engineering of novel flower color in tree peonies. In this study, we conducted a large-scale transcriptome analysis based on Illumina HiSeq sequencing of cDNA libraries generated from yellow and purple-red P. delavayi petals. A total of 90,202 unigenes were obtained by de novo assembly, with an average length of 721 nt. Using Blastx, 44,811 unigenes (49.68%) were found to have significant similarity to accessions in the NR, NT, and Swiss-Prot databases. We also examined COG, GO and KEGG annotations to better understand the functions of these unigenes. Further analysis of the two digital transcriptomes revealed that 6,855 unigenes were differentially expressed between yellow and purple-red flower petals, with 3,430 up-regulated and 3,425 down-regulated. According to the RNA-Seq data and qRT-PCR analysis, we proposed that four up-regulated key structural genes, including F3H, DFR, ANS and 3GT, might play an important role in purple-red petal pigmentation, while high co-expression of THC2'GT, CHI and FNS II ensures the accumulation of pigments contributing to the yellow color. We also found 50 differentially expressed transcription factors that might be involved in flavonoid biosynthesis. This study is the first to report genetic information for P. delavayi. The large number of gene sequences produced by transcriptome sequencing and the candidate genes identified using pathway mapping and expression profiles will provide a valuable resource for future association studies aimed at better understanding the molecular mechanisms underlying flower pigmentation in tree peonies. PMID:26267644

First results from the IllustrisTNG simulations: the galaxy colour bimodality

NASA Astrophysics Data System (ADS)

Nelson, Dylan; Pillepich, Annalisa; Springel, Volker; Weinberger, Rainer; Hernquist, Lars; Pakmor, Rüdiger; Genel, Shy; Torrey, Paul; Vogelsberger, Mark; Kauffmann, Guinevere; Marinacci, Federico; Naiman, Jill

2018-03-01

We introduce the first two simulations of the IllustrisTNG project, a next generation of cosmological magnetohydrodynamical simulations, focusing on the optical colours of galaxies. We explore TNG100, a rerun of the original Illustris box, and TNG300, which includes 2 × 25003 resolution elements in a volume 20 times larger. Here, we present first results on the galaxy colour bimodality at low redshift. Accounting for the attenuation of stellar light by dust, we compare the simulated (g - r) colours of 109 < M⋆/M⊙ < 1012.5 galaxies to the observed distribution from the Sloan Digital Sky Survey. We find a striking improvement with respect to the original Illustris simulation, as well as excellent quantitative agreement with the observations, with a sharp transition in median colour from blue to red at a characteristic M⋆ ˜ 1010.5 M⊙. Investigating the build-up of the colour-mass plane and the formation of the red sequence, we demonstrate that the primary driver of galaxy colour transition is supermassive black hole feedback in its low accretion state. Across the entire population the median colour transition time-scale Δtgreen is ˜1.6 Gyr, a value which drops for increasingly massive galaxies. We find signatures of the physical process of quenching: at fixed stellar mass, redder galaxies have lower star formation rates, gas fractions, and gas metallicities; their stellar populations are also older and their large-scale interstellar magnetic fields weaker than in bluer galaxies. Finally, we measure the amount of stellar mass growth on the red sequence. Galaxies with M⋆ > 1011 M⊙ which redden at z < 1 accumulate on average ˜25 per cent of their final z = 0 mass post-reddening; at the same time, ˜18 per cent of such massive galaxies acquire half or more of their final stellar mass while on the red sequence.

Effect of vacuum and modified atmosphere packaging on the microbiological, chemical and sensory properties of tropical red drum (Sciaenops ocellatus) fillets stored at 4°C.

PubMed

Silbande, Adèle; Adenet, Sandra; Chopin, Christine; Cornet, Josiane; Smith-Ravin, Juliette; Rochefort, Katia; Leroi, Françoise

2018-02-02

The effect of vacuum (VP - 4°C) and CO 2 /N 2 -atmosphere (MAP - 4°C) packaging on the quality of red drum fillets compared with whole gutted iced fish was investigated. A metagenomic approach, bacterial enumeration and isolation, biochemical and sensory analyses were carried out. The organoleptic rejection of whole fish was observed at day 15 whereas VP and MAP fillets appeared unacceptable only after 29days. At these dates, total mesophilic counts reached 10 7 -10 8 CFU g -1 . According to Illumina MiSeq sequencing, Arthrobacter, Chryseobacterium, Brevibacterium, Staphylococcus and Kocuria were the main genera of the fresh red drum fillets. At the sensory rejection time, lactic acid bacteria (LAB), particularly Carnobacterium sp., dominated the microbiota of both types of packaging. The pH value of fresh samples was between 5.96 and 6.37 and did not vary greatly in all trials. Total volatile basic nitrogen (TVBN) and trimethylamine (TMA) concentrations were low and not represent reliable indicators of the spoilage, contrary to some biogenic amines (cadaverine, putrescine and tyramine). Chilled packed fillets of red drum have an extended shelf-life compared to whole gutted iced fish. Overall, few differences in sensory and microbial quality were observed between the VP and MAP samples. Next-Generation Sequencing (NGS) provided data on the microbiota of a tropical fish. Copyright © 2017 Elsevier B.V. All rights reserved.

Ammonia oxidation-dependent growth of group I.1b Thaumarchaeota in acidic red soil microcosms.

PubMed

Wu, Yucheng; Conrad, Ralf

2014-07-01

Accumulating evidence suggests that Thaumarchaeota may control nitrification in acidic soils. However, the composition of the thaumarchaeotal communities and their functioning is not well known. Therefore, we studied nitrification activity in relation to abundance and composition of Thaumarchaeota in an acidic red soil from China, using microcosms incubated with and without cellulose amendment. Cellulose was selected to simulate the input of crop residues used to increase soil fertility by local farming. Accumulation of NO3-(-N) was correlated with the growth of Thaumarchaeota as determined by qPCR of 16S rRNA and ammonia monooxygenase (amoA) genes. Both nitrification activity and thaumarchaeotal growth were inhibited by acetylene. They were also inhibited by cellulose amendment, possibly due to the depletion of ammonium by enhanced heterotrophic assimilation. These results indicated that growth of Thaumarchaeota was dependent on ammonia oxidation. The thaumarchaeotal 16S rRNA gene sequences in the red soil were dominated by a clade related to soil fosmid clone 29i4 within the group I.1b, which is widely distributed but so far uncultured. The archaeal amoA sequences were mainly related to the Nitrososphaera sister cluster. These observations suggest that fosmid clone 29i4 and Nitrososphaera sister cluster represent the same group of Thaumarchaeota and dominate ammonia oxidation in acidic red soil. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

The formation and build-up of the red-sequence over the past 9 Gyr in VIPERS

NASA Astrophysics Data System (ADS)

Fritz, Alexander; Abbas, U.; Adami, C.; Arnouts, S.; Bel, J.; Bolzonella, M.; Bottini, D.; Branchini, E.; Burden, A.; Cappi, A.; Coupon, J.; Cucciati, O.; Davidzon, I.; De Lucia, G.; de la Torre, S.; Di Porto, C.; Franzetti, P.; Fumana, M.; Garilli, B.; Granett, B. R.; Guzzo, L.; Ilbert, O.; Iovino, A.; Krywult, J.; Le Brun, V.; Le Fèvre, O.; Maccagni, D.; Małek, K.; Marchetti, A.; Marinoni, C.; Marulli, F.; McCracken, H. J.; Mellier, Y.; Moscardini, L.; Nichol, R. C.; Paioro, L.; Peacock, J. A.; Percival, W. J.; Polletta, M.; Pollo, A.; Scodeggio, M.; Tasca, L. A. M.; Tojeiro, R.; Vergani, D.; Zamorani, G.; Zanichelli, A.; VIPERS Team

2015-02-01

We present the Luminosity Function (LF) and Colour-Magnitude Relation (CMR) using ~45000 galaxies drawn from the VIMOS Public Extragalactic Redshift Survey (VIPERS). Using different selection criteria, we define several samples of early-type galaxies and explore their impact on the evolution of the red-sequence (RS) and the effects of dust. Our results suggest a rapid build-up of the RS within a short time scale. We find a rise in the number density of early-type galaxies and a strong evolution in LF and CMR. Massive galaxies exist already 9 Gyr ago and experience an efficient quenching of their star formation at z = 1, followed by a passive evolution with only limited merging activity. In contrast, low-mass galaxies indicate a different mass assembly history and cause a slow build-up of the CMR over cosmic time.

Air Force Dynamic Mechanical Analysis of NATO Round Robin Propellant Testing for Development of AOP-4717

DTIC Science & Technology

2015-09-23

Round Robin Propellant Testing for Development of AOP-4717 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...area code) N/A Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std. 239.18 0 Air Force Dynamic Mechanical Analysis of NATO Round Robin ...the clamps are tight at the coldest temperature. • Long tests such as the frequency sweep sequences prescribed in this round robin may be

Development and evaluation of a fault-tolerant multiprocessor (FTMP) computer. Volume 1: FTMP principles of operation

NASA Technical Reports Server (NTRS)

Smith, T. B., Jr.; Lala, J. H.

1983-01-01

The basic organization of the fault tolerant multiprocessor, (FTMP) is that of a general purpose homogeneous multiprocessor. Three processors operate on a shared system (memory and I/O) bus. Replication and tight synchronization of all elements and hardware voting is employed to detect and correct any single fault. Reconfiguration is then employed to repair a fault. Multiple faults may be tolerated as a sequence of single faults with repair between fault occurrences.

The environmental impacts on the star formation main sequence: An Hα study of the newly discovered rich cluster at z = 1.52

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

Koyama, Yusei; Kodama, Tadayuki; Tadaki, Ken-ichi

2014-07-01

We report the discovery of a strong over-density of galaxies in the field of a radio galaxy at z = 1.52 (4C 65.22) based on our broadband and narrow-band (Hα) photometry with the Subaru Telescope. We find that Hα emitters are located in the outskirts of the density peak (cluster core) dominated by passive red-sequence galaxies. This resembles the situation in lower-redshift clusters, suggesting that the newly discovered structure is a well-evolved rich galaxy cluster at z = 1.5. Our data suggest that the color-density and stellar mass-density relations are already in place at z ∼ 1.5, mostly driven bymore » the passive red massive galaxies residing within r{sub c} ≲ 200 kpc from the cluster core. These environmental trends almost disappear when we consider only star-forming (SF) galaxies. We do not find SFR-density or SSFR-density relations amongst SF galaxies, and the location of the SF main sequence does not significantly change with environment. Nevertheless, we find a tentative hint that star-bursting galaxies (up-scattered objects from the main sequence) are preferentially located in a small group at ∼1 Mpc away from the main body of the cluster. We also argue that the scatter of the SF main sequence could be dependent on the distance to the nearest neighboring galaxy.« less

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

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

Torella, JP; Boehm, CR; Lienert, F

2013-12-28

In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminatormore » parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.« less

Sequence Dependencies of DNA Deformability and Hydration in the Minor Groove

PubMed Central

Yonetani, Yoshiteru; Kono, Hidetoshi

2009-01-01

Abstract DNA deformability and hydration are both sequence-dependent and are essential in specific DNA sequence recognition by proteins. However, the relationship between the two is not well understood. Here, systematic molecular dynamics simulations of 136 DNA sequences that differ from each other in their central tetramer revealed that sequence dependence of hydration is clearly correlated with that of deformability. We show that this correlation can be illustrated by four typical cases. Most rigid basepair steps are highly likely to form an ordered hydration pattern composed of one water molecule forming a bridge between the bases of distinct strands, but a few exceptions favor another ordered hydration composed of two water molecules forming such a bridge. Steps with medium deformability can display both of these hydration patterns with frequent transition. Highly flexible steps do not have any stable hydration pattern. A detailed picture of this correlation demonstrates that motions of hydration water molecules and DNA bases are tightly coupled with each other at the atomic level. These results contribute to our understanding of the entropic contribution from water molecules in protein or drug binding and could be applied for the purpose of predicting binding sites. PMID:19686662

Non-tuberculous Mycobacteriosis with T-cell Lymphoma in a Red Panda (Ailurus fulgens).

PubMed

Fuke, N; Hirai, T; Makimura, N; Goto, Y; Habibi, W A; Ito, S; Trang, N T; Koshino, K; Takeda, M; Yamaguchi, R

2016-01-01

A 9-year-old male red panda (Ailurus fulgens) became emaciated and died. Necropsy examination revealed systemic lymphadenomegaly. The liver, lungs and left kidney contained multifocal yellow nodules. Microscopical examination revealed granulomatous inflammation in the liver, lungs, kidney, spleen and lymph nodes, with numerous acid-fast bacilli. Sequencing of genetic material isolated from the tissues classified the pathogen as Mycobacterium gastri. Lymphoma was found in the liver, lungs, kidney and lymph nodes. The neoplastic cells were strongly labelled for expression of CD3, Ki67 and proliferating cell nuclear antigen by immunohistochemistry. This is the first report of M. gastri infection with T-cell lymphoma in a red panda. Copyright © 2016 Elsevier Ltd. All rights reserved.

X-rays from accretion of red giant winds

NASA Technical Reports Server (NTRS)

Jura, M.; Helfand, D. J.

1984-01-01

X-ray observations of the late-type red giants Mira and R Aqr obtained with the Einstein Observatory are presented, and the general problems of white dwarf accretion from late-type giant winds is considered. The extremely low measured luminosities obtained for the two systems leads to the conclusion that the companions of Mira and R Aqr are most likely low-mass main sequence objects rather than white dwarfs as is usually assumed. The expected X-ray luminosities of true red giant/white dwarf systems are considered, and it is concluded that far too few have been detected if the canonical accretion scenario is adopted. A possible explanation of this situation in terms of grain-dominated Eddington-limited accretion is proposed.

DISCOVERY OF A RED GIANT WITH SOLAR-LIKE OSCILLATIONS IN AN ECLIPSING BINARY SYSTEM FROM KEPLER SPACE-BASED PHOTOMETRY

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

Hekker, S.; Debosscher, J.; De Ridder, J.

2010-04-20

Oscillating stars in binary systems are among the most interesting stellar laboratories, as these can provide information on the stellar parameters and stellar internal structures. Here we present a red giant with solar-like oscillations in an eclipsing binary observed with the NASA Kepler satellite. We compute stellar parameters of the red giant from spectra and the asteroseismic mass and radius from the oscillations. Although only one eclipse has been observed so far, we can already determine that the secondary is a main-sequence F star in an eccentric orbit with a semi-major axis larger than 0.5 AU and orbital period longermore » than 75 days.« less

Gravity modes as a way to distinguish between hydrogen- and helium-burning red giant stars.

PubMed

Bedding, Timothy R; Mosser, Benoit; Huber, Daniel; Montalbán, Josefina; Beck, Paul; Christensen-Dalsgaard, Jørgen; Elsworth, Yvonne P; García, Rafael A; Miglio, Andrea; Stello, Dennis; White, Timothy R; De Ridder, Joris; Hekker, Saskia; Aerts, Conny; Barban, Caroline; Belkacem, Kevin; Broomhall, Anne-Marie; Brown, Timothy M; Buzasi, Derek L; Carrier, Fabien; Chaplin, William J; Di Mauro, Maria Pia; Dupret, Marc-Antoine; Frandsen, Søren; Gilliland, Ronald L; Goupil, Marie-Jo; Jenkins, Jon M; Kallinger, Thomas; Kawaler, Steven; Kjeldsen, Hans; Mathur, Savita; Noels, Arlette; Aguirre, Victor Silva; Ventura, Paolo

2011-03-31

Red giants are evolved stars that have exhausted the supply of hydrogen in their cores and instead burn hydrogen in a surrounding shell. Once a red giant is sufficiently evolved, the helium in the core also undergoes fusion. Outstanding issues in our understanding of red giants include uncertainties in the amount of mass lost at the surface before helium ignition and the amount of internal mixing from rotation and other processes. Progress is hampered by our inability to distinguish between red giants burning helium in the core and those still only burning hydrogen in a shell. Asteroseismology offers a way forward, being a powerful tool for probing the internal structures of stars using their natural oscillation frequencies. Here we report observations of gravity-mode period spacings in red giants that permit a distinction between evolutionary stages to be made. We use high-precision photometry obtained by the Kepler spacecraft over more than a year to measure oscillations in several hundred red giants. We find many stars whose dipole modes show sequences with approximately regular period spacings. These stars fall into two clear groups, allowing us to distinguish unambiguously between hydrogen-shell-burning stars (period spacing mostly ∼ 50 seconds) and those that are also burning helium (period spacing ∼ 100 to 300 seconds).

Use of red mud (bauxite residue) for the retention of aqueous inorganic mercury(II).

PubMed

Rubinos, David A; Barral, María Teresa

2015-11-01

The effectiveness of the oxide-rich residue from bauxite refining (red mud) to remove inorganic Hg(II) from aqueous solutions was assessed. The aspects studied comprised the kinetics of the process (t = 1 min-24 h), the effect of pH (3.5-11.5), the interacting effect between salt concentration (0.01-1 M NaNO3) and pH and the Hg(II) sorption isotherm. Hg leaching from spent red mud was evaluated using the toxicity characteristics leaching procedure (TCLP) method. The sorption of Hg(II) onto red mud was very fast, with most of Hg(II) (97.0-99.7%) being removed from 0.5-50 μM Hg solutions in few minutes. The kinetic process was best described by Ho's pseudo-second order equation, pointing to chemisorption as the rate controlling step. Hg(II) sorption efficiency was very high (% removal between 93.9 and 99.8%) within all the studied pH range (3.5-11.5) and added Hg concentrations (5 and 50 μM), being optimal at pH 5-8 and decreasing slightly at both lowest and highest pH. The effect of background electrolyte concentration suggests specific sorption as the main interaction mechanism between Hg(II) and red mud, but the increasing non-sorbed Hg concentrations at low and high pH for higher electrolyte concentrations also revealed the contribution of an electrostatic component to the process. The sorption isotherm showed the characteristic shape of high affinity sorbents, and it was better described by the Redlich-Peterson and Freundlich equations, which are models that assume sorbent heterogeneity and involvement of more than one mechanism. The estimated Hg(II) sorption capacity from the Langmuir equation (q m ~9 mmol/kg) was comparable to those of some inorganic commercial sorbents but lower than most bio- or specifically designed sorbents. The leachability of retained Hg(II) from spent red mud (0.02, 0.25 and 2.42 mmol Hg/kg sorbed concentration) was low (0.28, 1.15 and 2.23 μmol/kg, respectively) and accounted for 1.2, 0.5 and 0.1% of previously sorbed Hg, indicating that Hg(II) is tightly bound by red mud once sorbed.

mir-125a-5p-mediated Regulation of Lfng is Essential for the Avian Segmentation Clock

PubMed Central

Riley, Maurisa F.; Bochter, Matthew S.; Wahi, Kanu; Nuovo, Gerard J.; Cole, Susan E.

2013-01-01

Summary Somites are embryonic precursors of the axial skeleton and skeletal muscles, and establish the segmental vertebrate body plan. Somitogenesis is controlled in part by a segmentation clock that requires oscillatory expression of genes including Lunatic fringe (Lfng). Oscillatory genes must be tightly regulated both at the transcriptional and post-transcriptional levels for proper clock function. Here we demonstrate that microRNA-mediated regulation of Lfng is essential for proper segmentation during chick somitogenesis. We find that mir-125a-5p targets evolutionarily conserved sequences in the Lfng 3′UTR, and that preventing interactions between mir-125a-5p and Lfng transcripts in vivo causes abnormal segmentation and perturbs clock activity. This provides strong evidence that miRNAs function in the post-transcriptional regulation of oscillatory genes in the segmentation clock. Further, this demonstrates that the relatively subtle effects of miRNAs on target genes can have broad effects in developmental situations that have critical requirements for tight post-transcriptional regulation. PMID:23484856

Prediction of pi-turns in proteins using PSI-BLAST profiles and secondary structure information.

PubMed

Wang, Yan; Xue, Zhi-Dong; Shi, Xiao-Hong; Xu, Jin

2006-09-01

Due to the structural and functional importance of tight turns, some methods have been proposed to predict gamma-turns, beta-turns, and alpha-turns in proteins. In the past, studies of pi-turns were made, but not a single prediction approach has been developed so far. It will be useful to develop a method for identifying pi-turns in a protein sequence. In this paper, the support vector machine (SVM) method has been introduced to predict pi-turns from the amino acid sequence. The training and testing of this approach is performed with a newly collected data set of 640 non-homologous protein chains containing 1931 pi-turns. Different sequence encoding schemes have been explored in order to investigate their effects on the prediction performance. With multiple sequence alignment and predicted secondary structure, the final SVM model yields a Matthews correlation coefficient (MCC) of 0.556 by a 7-fold cross-validation. A web server implementing the prediction method is available at the following URL: http://210.42.106.80/piturn/.

An improved pulse sequence and inversion algorithm of T2 spectrum

NASA Astrophysics Data System (ADS)

Ge, Xinmin; Chen, Hua; Fan, Yiren; Liu, Juntao; Cai, Jianchao; Liu, Jianyu

2017-03-01

The nuclear magnetic resonance transversal relaxation time is widely applied in geological prospecting, both in laboratory and downhole environments. However, current methods used for data acquisition and inversion should be reformed to characterize geological samples with complicated relaxation components and pore size distributions, such as samples of tight oil, gas shale, and carbonate. We present an improved pulse sequence to collect transversal relaxation signals based on the CPMG (Carr, Purcell, Meiboom, and Gill) pulse sequence. The echo spacing is not constant but varies in different windows, depending on prior knowledge or customer requirements. We use the entropy based truncated singular value decomposition (TSVD) to compress the ill-posed matrix and discard small singular values which cause the inversion instability. A hybrid algorithm combining the iterative TSVD and a simultaneous iterative reconstruction technique is implemented to reach the global convergence and stability of the inversion. Numerical simulations indicate that the improved pulse sequence leads to the same result as CPMG, but with lower echo numbers and computational time. The proposed method is a promising technique for geophysical prospecting and other related fields in future.

Kinact: a computational approach for predicting activating missense mutations in protein kinases.

PubMed

Rodrigues, Carlos H M; Ascher, David B; Pires, Douglas E V

2018-05-21

Protein phosphorylation is tightly regulated due to its vital role in many cellular processes. While gain of function mutations leading to constitutive activation of protein kinases are known to be driver events of many cancers, the identification of these mutations has proven challenging. Here we present Kinact, a novel machine learning approach for predicting kinase activating missense mutations using information from sequence and structure. By adapting our graph-based signatures, Kinact represents both structural and sequence information, which are used as evidence to train predictive models. We show the combination of structural and sequence features significantly improved the overall accuracy compared to considering either primary or tertiary structure alone, highlighting their complementarity. Kinact achieved a precision of 87% and 94% and Area Under ROC Curve of 0.89 and 0.92 on 10-fold cross-validation, and on blind tests, respectively, outperforming well established tools (P < 0.01). We further show that Kinact performs equally well on homology models built using templates with sequence identity as low as 33%. Kinact is freely available as a user-friendly web server at http://biosig.unimelb.edu.au/kinact/.

Leg 67: the Deep Sea Drilling Project Mid-America Trench transect off Guatemala.

USGS Publications Warehouse

von Huene, Roland E.

1980-01-01

Drilling on the Cocos plate recovered a basal chalk sequence deposited during early and mid-Miocene time, a short interval of abyssal red clay, and an upper sequence of late Miocene and younger sediment deposited within an area influenced by a terrigenous source. In the trench, a mud and sand fill less than 400,000 yr old overlies the oceanic sequence. The entire section shows no evidence of compressive deformation. In contrast, the section cored on the trench's landward slope 3 km from the trench axis is affected by tectonism. The section contains a Cretaceous to Pliocene claystone sequence capped by Pliocene to Quaternary hemipelagic slope deposits.- from Authors

Highly Conserved Mitochondrial Genomes among Multicellular Red Algae of the Florideophyceae

PubMed Central

Yang, Eun Chan; Kim, Kyeong Mi; Kim, Su Yeon; Lee, JunMo; Boo, Ga Hun; Lee, Jung-Hyun; Nelson, Wendy A.; Yi, Gangman; Schmidt, William E.; Fredericq, Suzanne; Boo, Sung Min; Bhattacharya, Debashish; Yoon, Hwan Su

2015-01-01

Two red algal classes, the Florideophyceae (approximately 7,100 spp.) and Bangiophyceae (approximately 193 spp.), comprise 98% of red algal diversity in marine and freshwater habitats. These two classes form well-supported monophyletic groups in most phylogenetic analyses. Nonetheless, the interordinal relationships remain largely unresolved, in particular in the largest subclass Rhodymeniophycidae that includes 70% of all species. To elucidate red algal phylogenetic relationships and study organelle evolution, we determined the sequence of 11 mitochondrial genomes (mtDNA) from 5 florideophycean subclasses. These mtDNAs were combined with existing data, resulting in a database of 25 florideophytes and 12 bangiophytes (including cyanidiophycean species). A concatenated alignment of mt proteins was used to resolve ordinal relationships in the Rhodymeniophycidae. Red algal mtDNA genome comparisons showed 47 instances of gene rearrangement including 12 that distinguish Bangiophyceae from Hildenbrandiophycidae, and 5 that distinguish Hildenbrandiophycidae from Nemaliophycidae. These organelle data support a rapid radiation and surprisingly high conservation of mtDNA gene syntheny among the morphologically divergent multicellular lineages of Rhodymeniophycidae. In contrast, we find extensive mitochondrial gene rearrangements when comparing Bangiophyceae and Florideophyceae and multiple examples of gene loss among the different red algal lineages. PMID:26245677

Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles

NASA Astrophysics Data System (ADS)

Edwards, Ceiridwen J.; Soulsbury, Carl D.; Statham, Mark J.; Ho, Simon Y. W.; Wall, Dave; Dolf, Gaudenz; Iossa, Graziella; Baker, Phillip J.; Harris, Stephen; Sacks, Benjamin N.; Bradley, Daniel G.

2012-12-01

Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox (Vulpes vulpes), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum. We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe.

Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles.

PubMed

Edwards, Ceiridwen J; Soulsbury, Carl D; Statham, Mark J; Ho, Simon Y W; Wall, Dave; Dolf, Gaudenz; Iossa, Graziella; Baker, Phillip J; Harris, Stephen; Sacks, Benjamin N; Bradley, Daniel G

2012-12-04

Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox ( Vulpes vulpes ), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum. We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe.

HUBBLE SPACE TELESCOPE CONSTRAINTS ON THE WINDS AND ASTROSPHERES OF RED GIANT STARS

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

Wood, Brian E.; Müller, Hans-Reinhard; Harper, Graham M., E-mail: brian.wood@nrl.navy.mil

We report on an ultraviolet spectroscopic survey of red giants observed by the Hubble Space Telescope , focusing on spectra of the Mg ii h and k lines near 2800 Å in order to study stellar chromospheric emission, winds, and astrospheric absorption. We focus on spectral types between K2 III and M5 III, a spectral type range with stars that are noncoronal, but possessing strong, chromospheric winds. We find a very tight relation between Mg ii surface flux and photospheric temperature, supporting the notion that all K2-M5 III stars are emitting at a basal flux level. Wind velocities ( Vmore » {sub w} ) are generally found to decrease with spectral type, with V {sub w} decreasing from ∼40 km s{sup −1} at K2 III to ∼20 km s{sup −1} at M5 III. We find two new detections of astrospheric absorption, for σ Pup (K5 III) and γ Eri (M1 III). This absorption signature had previously only been detected for α Tau (K5 III). For the three astrospheric detections, the temperature of the wind after the termination shock (TS) correlates with V {sub w} , but is lower than predicted by the Rankine–Hugoniot shock jump conditions, consistent with the idea that red giant TSs are radiative shocks rather than simple hydrodynamic shocks. A full hydrodynamic simulation of the γ Eri astrosphere is provided to explore this further.« less

Recovering the systemic redshift of galaxies from their Lyman-alpha line profile

NASA Astrophysics Data System (ADS)

Verhamme, A.; Garel, T.; Ventou, E.; Contini, T.; Bouché, N.; Herenz, E. C.; Richard, J.; Bacon, R.; Schmidt, K. B.; Maseda, M.; Marino, R. A.; Brinchmann, J.; Cantalupo, S.; Caruana, J.; Clément, B.; Diener, C.; Drake, A. B.; Hashimoto, T.; Inami, H.; Kerutt, J.; Kollatschny, W.; Leclercq, F.; Patrício, V.; Schaye, J.; Wisotzki, L.; Zabl, J.

2018-04-01

The Lyman alpha (Lyα) line of Hydrogen is a prominent feature in the spectra of star-forming galaxies, usually redshifted by a few hundreds of km s-1 compared to the systemic redshift. This large offset hampers follow-up surveys, galaxy pair statistics and correlations with quasar absorption lines when only Lyα is available. We propose diagnostics that can be used to recover the systemic redshift directly from the properties of the Lyα line profile. We use spectroscopic observations of Lyman-Alpha Emitters (LAEs) for which a precise measurement of the systemic redshift is available. Our sample contains 13 sources detected between z ≈ 3 and z ≈ 6 as part of various Multi Unit Spectroscopic Explorer (MUSE) Guaranteed Time Observations (GTO). We also include a compilation of spectroscopic Lyα data from the literature spanning a wide redshift range (z ≈ 0 - 8). First, restricting our analysis to double-peaked Lyα spectra, we find a tight correlation between the velocity offset of the red peak with respect to the systemic redshift, V_peak^red, and the separation of the peaks. Secondly, we find a correlation between V_peak^red and the full width at half maximum of the Lyα line. Fitting formulas, to estimate systemic redshifts of galaxies with an accuracy of ≤100 km s-1 when only the Lyα emission line is available, are given for the two methods.

Peptide de novo sequencing of mixture tandem mass spectra.

PubMed

Gorshkov, Vladimir; Hotta, Stéphanie Yuki Kolbeck; Verano-Braga, Thiago; Kjeldsen, Frank

2016-09-01

The impact of mixture spectra deconvolution on the performance of four popular de novo sequencing programs was tested using artificially constructed mixture spectra as well as experimental proteomics data. Mixture fragmentation spectra are recognized as a limitation in proteomics because they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co-isolation and thus prone to false identifications. The deconvolution approach matched complementary b-, y-ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co-isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced peptides. The improvement was in the range of 20-35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight candidate peptide score distribution and high sensitivity to small changes in the mass spectrum introduced by the employed deconvolution method could explain some of the missing peptide identifications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gene Expression Profiling of Development and Anthocyanin Accumulation in Kiwifruit (Actinidia chinensis) Based on Transcriptome Sequencing

PubMed Central

Zeng, Shaohua; Xiao, Gong; Wang, Gan; Wang, Ying; Peng, Ming; Huang, Hongwen

2015-01-01

Red-fleshed kiwifruit (Actinidia chinensis Planch. ‘Hongyang’) is a promising commercial cultivar due to its nutritious value and unique flesh color, derived from vitamin C and anthocyanins. In this study, we obtained transcriptome data of ‘Hongyang’ from seven developmental stages using Illumina sequencing. We mapped 39–54 million reads to the recently sequenced kiwifruit genome and other databases to define gene structure, to analyze alternative splicing, and to quantify gene transcript abundance at different developmental stages. The transcript profiles throughout red kiwifruit development were constructed and analyzed, with a focus on the biosynthesis and metabolism of compounds such as phytohormones, sugars, starch and L-ascorbic acid, which are indispensable for the development and formation of quality fruit. Candidate genes for these pathways were identified through MapMan and phylogenetic analysis. The transcript levels of genes involved in sucrose and starch metabolism were consistent with the change in soluble sugar and starch content throughout kiwifruit development. The metabolism of L-ascorbic acid was very active, primarily through the L-galactose pathway. The genes responsible for the accumulation of anthocyanin in red kiwifruit were identified, and their expression levels were investigated during kiwifruit development. This survey of gene expression during kiwifruit development paves the way for further investigation of the development of this uniquely colored and nutritious fruit and reveals which factors are needed for high quality fruit formation. This transcriptome data and its analysis will be useful for improving kiwifruit genome annotation, for basic fruit molecular biology research, and for kiwifruit breeding and improvement. PMID:26301713

IMPLICATIONS OF RAPID CORE ROTATION IN RED GIANTS FOR INTERNAL ANGULAR MOMENTUM TRANSPORT IN STARS

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

Tayar, Jamie; Pinsonneault, Marc H., E-mail: tayar.1@osu.edu

2013-09-20

Core rotation rates have been measured for red giant stars using asteroseismology. These data, along with helioseismic measurements and open cluster spin-down studies, provide powerful clues about the nature and timescale for internal angular momentum transport in stars. We focus on two cases: the metal-poor red giant KIC 7341231 ({sup O}tto{sup )} and intermediate-mass core helium burning stars. For both, we examine limiting case studies for angular momentum coupling between cores and envelopes under the assumption of rigid rotation on the main sequence. We discuss the expected pattern of core rotation as a function of mass and radius. In themore » case of Otto, strong post-main-sequence coupling is ruled out and the measured core rotation rate is in the range of 23-33 times the surface value expected from standard spin-down models. The minimum coupling timescale (0.17-0.45 Gyr) is significantly longer than that inferred for young open cluster stars. This implies ineffective internal angular momentum transport in early first ascent giants. By contrast, the core rotation rates of evolved secondary clump stars are found to be consistent with strong coupling given their rapid main-sequence rotation. An extrapolation to the white dwarf regime predicts rotation periods between 330 and 0.0052 days, depending on mass and decoupling time. We identify two key ingredients that explain these features: the presence of a convective core and inefficient angular momentum transport in the presence of larger mean molecular weight gradients. Observational tests that can disentangle these effects are discussed.« less

Spectral lines behavior of Be I and Na I isoelectronic sequence in Debye plasma environment

NASA Astrophysics Data System (ADS)

Chaudhuri, Rajat K.; Chattopadhyay, Sudip; Sinha Mahapatra, Uttam

2012-08-01

We report the plasma screening effect on the first ionization potential (IP) and [He]2s2(1S0)→[He]2s2p /2s3p allowed (P11) and inter-combination transitions (P31) in some selected Be-like ions. In addition, we investigate the spectral properties of [Ne]3s (2S1/2)→[Ne]np(2P1/2 and P23/2 for n = 3, 4) transitions in Ca X and Fe XVI ions (Na I isoelectronic sequence) and [He]3s(2S1/2)→[He]np(2P1/2 and P23/2 for n = 2, 3) transitions in Li, B II, and N IV (Li I isoelectronic sequence) under plasma environment. The state-of-the-art relativistic coupled cluster calculations using the Debye model of plasma for electron-nucleus interaction show that (a) the ionization potential decreases sharply with increasing plasma strength and (b) the gap between the [He]2s2(1S0)→[He]2s2p(1,3P1) energy levels increases with increasing plasma potential and nuclear charge. It is found that the [He]2s2 (1S0)→2s3p(1,3P1) transition energy decreases uniformly with increasing plasma potential and nuclear charge. In other words, the spectral lines associated with 2s-2p (i.e., Δn=0, where n corresponds to principle quantum number) transitions in Be I isoelectronic sequence exhibit a blue-shift (except for Be I, B II, and the lowest inter-combination line in C III, which exhibit a red-shift), whereas those associated with 2s-3p (i.e., Δn≠0) transitions are red-shifted. Similar trend is observed in Li I and Na I isoelectronic sequences, where spectral lines associated with Δn=0 (Δn≠0) are blue-shifted (red-shifted). The effect of Coulomb screening on the spectral lines of ions subjected to plasma is also addressed.

Kinematics of Stars from the TGAS (Gaia DR1) Catalogue

NASA Astrophysics Data System (ADS)

Vityazev, V. V.; Popov, A. V.; Tsvetkov, A. S.; Petrov, S. D.; Trofimov, D. A.; Kiyaev, V. I.

2018-04-01

Based on the stellar proper motions of the TGAS (Gaia DR1) catalogue, we have analyzed the velocity field of main-sequence stars and red giants from the TGAS catalogue with heliocentric distances up to 1.5 kpc. We have obtained four variants of kinematic parameters corresponding to different methods of calculating the distances from the parallaxes of stars measured with large relative errors. We have established that within the Ogorodnikov-Milne model changing the variant of distances affects significantly only the solar velocity components relative to the chosen centroid of stars, provided that the solution is obtained in narrow ranges of distances (0.1 kpc). The estimates of all the remaining kinematic parameters change little. This allows the Oort coefficients and related Galactic rotation parameters as well as all the remaining Ogorodnikov-Milne model parameters (except for the solar terms) to be reliably estimated irrespective of the parallax measurement accuracy. The main results obtained from main-sequence stars in the range of distances from 0.1 to 1.5 kpc are: A = 16.29 ± 0.06 km s-1 kpc-1, B = -11.90 ± 0.05 km s-1 kpc-1, C = -2.99 ± 0.06 km s-1 kpc-1, K = -4.04 ± 0.16 km s-1 kpc-1, and the Galactic rotation period P = 217.41 ± 0.60 Myr. The analogous results obtained from red giants in the range from 0.2 to 1.6 kpc are: the Oort constants A = 13.32 ± 0.09 km s-1 kpc-1, B = -12.71 ± 0.06 km s-1 kpc-1, C = -2.04 ± 0.08 km s-1 kpc-1, K = -2.72 ± 0.19 km s-1 kpc-1, and the Galactic rotation period P = 236.03 ± 0.98 Myr. The Galactic rotation velocity gradient along the radius vector (the slope of the Galactic rotation curve) is -4.32 ± 0.08 km s-1 kpc-1 for main-sequence stars and -0.61 ± 0.11 km s-1 kpc-1 for red giants. This suggests that the Galactic rotation velocity determined from main-sequence stars decreases with increasing distance from the Galactic center faster than it does for red giants.

Localization of Filipin-Sterol Complexes in the Membranes of Beta vulgaris Roots and Spinacia oleracea Chloroplasts 1

PubMed Central

Moeller, Curt H.; Mudd, J. Brian

1982-01-01

Filipin was used as a cytochemical probe for membrane sterols in the root storage tissue of the red beet Beta vulgaris L. and the chloroplasts of Spinacia oleracea L. In unfixed beet tissue, filipin lysed the cells. Freeze-fracture replicas revealed that the filipin-sterol complexes were tightly aggregated in the plasma membrane, while in thin section the complexes corrugated the plasma membrane. If the cells were fixed with glutaraldehyde prior to the filipin treatment, the cell structure was preserved. Filipin-induced lesions were dispersed or clustered loosely in the plasma membrane. A few filipin-sterol complexes were observed in the tonoplast. In spinach chloroplasts, filipin-sterol complexes were limited to the outer membrane of the envelope and were not found in the inner membrane of the envelope or in the lamellar membranes. If the filipin-sterol complexes accurately mapped the distribution of membrane sterols, then sterol was located predominantly in the plasma membrane of the red beet and in the outer membrane of the chloroplast envelope. Furthermore, the sterol may be heterogenously distributed laterally in both these membranes. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:16662716

A procedure for the measurement of Oxygen Consumption Rates (OCRs) in red wines and some observations about the influence of wine initial chemical composition.

PubMed

Marrufo-Curtido, Almudena; Carrascón, Vanesa; Bueno, Mónica; Ferreira, Vicente; Escudero, Ana

2018-05-15

The rates at which wine consumes oxygen are important technological parameters for whose measurement there are not accepted procedures. In this work, volumes of 8 wines are contacted with controlled volumes of air in air-tight tubes containing oxygen-sensors and are further agitated at 25 °C until O 2 consumption is complete. Three exposure levels of O 2 were used: low (10 mg/L) and medium or high (18 or 32 mg/L plus the required amount to oxidize all wine SO 2 ). In each oxygen level, 2-4 independent segments following pseudo-first order kinetics were identified, plus an initial segment at which wine consumed O 2 very fast. Overall, multivariate data techniques identify six different Oxygen-Consumption-Rates (OCRs) as required to completely define wine O 2 consumption. Except the last one, all could be modeled from the wine initial chemical composition. Total acetaldehyde, Mn, Cu/Fe, blue and red pigments and gallic acid seem to be essential to determine these OCRs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Kit for the rapid preparation of .sup.99m Tc red blood cells

DOEpatents

Richards, Powell; Smith, Terry D.

1976-01-01

A method and sample kit for the preparation of .sup.99m Tc-labeled red blood cells in a closed, sterile system. A partially evacuated tube, containing a freeze-dried stannous citrate formulation with heparin as an anticoagulant, allows whole blood to be automatically drawn from the patient. The radioisotope is added at the end of the labeling sequence to minimize operator exposure. Consistent 97% yields in 20 minutes are obtained with small blood samples. Freeze-dried kits have remained stable after five months.

A white dwarf companion to the main-sequence star 4 Omicron(1) Orionis and the binary hypothesis for the origin of peculiar red giants

NASA Technical Reports Server (NTRS)

Ake, Thomas B.; Johnson, Hollis R.

1988-01-01

Ultraviolet spectra of the peculiar red giants (PRGs) called MS stars are investigated, and the discovery of a white dwarf (WD) companion to the MS star 4 Omicron(1) Orionis is reported. The observations and data analysis are discussed and compared with those for field WDs in order to derive parameters for the WD and the luminosity of the primary. Detection limits for the other MS stars investigated are derived, and the binary hypothesis for PRGs is reviewed.

Reptilian transferrins: evolution of disulphide bridges and conservation of iron-binding center.

PubMed

Ciuraszkiewicz, Justyna; Biczycki, Marian; Maluta, Aleksandra; Martin, Samuel; Watorek, Wiesław; Olczak, Mariusz

2007-07-01

Transferrins, found in invertebrates and vertebrates, form a physiologically important family of proteins playing a major role in iron acquisition and transport, defense against microbial pathogens, growth and differentiation. These proteins are bilobal in structure and each lobe is composed of two domains divided by a cleft harboring an iron atom. Vertebrate transferrins comprise of serotransferrins, lactoferrins and ovotransferrins. In mammals serotransferrins transport iron in physiological fluids and deliver it to cells, while lactoferrins scavenge iron, limiting its availability to invading microbes. In oviparous vertebrates there is only one transferrin gene, expressed either in the liver to be delivered to physiological fluids as serotransferrin, or in the oviduct with a final localization in egg white as ovotransferrin. Being products of one gene sero- and ovotransferrin are identical at the amino-acid sequence level but with different, cell specific glycosylation patterns. Our knowledge of the mechanisms of transferrin iron binding and release is based on sequence and structural data obtained for human serotransferrin and hen and duck ovotransferrins. No sequence information about other ovotransferrins was available until our recent publication of turkey, ostrich, and red-eared turtle (TtrF) ovotransferrin mRNA sequences [Ciuraszkiewicz, J., Olczak, M., Watorek, W., 2006. Isolation, cloning and sequencing of transferrins from red-eared turtle, African ostrich and turkey. Comp. Biochem. Physiol. 143 B, 301-310]. In the present paper, ten new reptilian mRNA transferrin sequences obtained from the Nile crocodile (NtrF), bearded dragon (BtrF), Cuban brown anole (AtrF), veiled and Mediterranean chameleons (VtrF and KtrF), sand lizard (StrF), leopard gecko (LtrF), Burmese python (PtrF), African house snake (HtrF), and grass snake (GtrF) are presented and analyzed. Nile crocodile and red-eared turtle transferrins have a disulphide bridge pattern identical to known bird homologues. A partially different disulphide bridge pattern was found in the Squamata (snakes and lizards). The possibility of a unique interdomain disulphide bridge was predicted for LtrF. Differences were found in iron-binding centers from those of previously known transferrins. Substitutions were found in the iron-chelating residues of StrF and TtrF and in the synergistic anion-binding residues of NtrF. In snakes, the transferrin (PtrF, HtrF and GtrF) N-lobe "dilysine trigger" occurring in all other known transferrins was not found, which indicates a different mechanism of iron release.

Development of a Tightly Controlled Off Switch for Saccharomyces cerevisiae Regulated by Camphor, a Low-Cost Natural Product

PubMed Central

Ikushima, Shigehito; Zhao, Yu; Boeke, Jef D.

2015-01-01

Here we describe the engineering of a distant homolog of the Tet repressor, CamR, isolated from Pseudomonas putida, that is regulated by camphor, a very inexpensive small molecule (at micromolar concentrations) for use in Saccharomyces cerevisiae. The repressor was engineered by expression from a constitutive yeast promoter, fusion to a viral activator protein cassette, and codon optimization. A suitable promoter responsive to the CamR fusion protein was engineered by embedding a P. putida operator binding sequence within an upstream activating sequence (UAS)-less CYC1 promoter from S. cerevisiae. The switch, named the Camphor-Off switch, activates expression of a reporter gene in camphor-free media and represses it with micromolar concentrations of camphor. PMID:26206350

Inhibitory activity of an extract from a marine bacterium Halomonas sp. HSB07 against the red-tide microalga Gymnodinium sp. (Pyrrophyta)

NASA Astrophysics Data System (ADS)

Liu, Juan; Li, Fuchao; Liu, Ling; Jiang, Peng; Liu, Zhaopu

2013-11-01

In recent years, red tides occurred frequently in coastal areas worldwide. Various methods based on the use of clay, copper sulfate, and bacteria have been successful in controlling red tides to some extent. As a new defensive agent, marine microorganisms are important sources of compounds with potent inhibitory bioactivities against red-tide microalgae, such as Gymnodinium sp. (Pyrrophyta). In this study, we isolated a marine bacterium, HSB07, from seawater collected from Hongsha Bay, Sanya, South China Sea. Based on its 16S rRNA gene sequence and biochemical characteristics, the isolated strain HSB07 was identified as a member of the genus Halomonas. A crude ethyl acetate extract of strain HSB07 showed moderate inhibition activity against Gymnodinium sp. in a bioactive prescreening experiment. The extract was further separated into fractions A, B, and C by silica gel column chromatography. Fractions B and C showed strong inhibition activities against Gymnodinium. This is the first report of inhibitory activity of secondary metabolites of a Halomonas bacterium against a red-tide-causing microalga.

Red giants: then and now

NASA Astrophysics Data System (ADS)

Faulkner, John

Fred Hoyle's work on the structure and evolution of red giants, particularly his pathbreaking contribution with Martin Schwarzschild (Hoyle and Schwarzschild 1955), is both lauded and critically assessed. In his later lectures and work with students in the early 1960s, Hoyle presented more physical ways of understanding some of the approximations used, and results obtained, in that seminal paper. Although later ideas by other investigators will be touched upon, Hoyle's viewpoint - that low-mass red giants are essentially white dwarfs with a serious mass-storage problem - is still extremely fruitful. Over the years, I have further developed his method of attack. Relatively recently, I have been able to deepen and broaden the approach, finally extending the theory to provide a unifying treatment of the structure of low-mass stars from the main sequence though both the red-giant and horizontal-branch phases of evolution. Many aspects of these stars that had remained puzzling, even mysterious, for decades have now fallen into place, and some questions have been answered that were not even posed before. With low-mass red giants as the simplest example, this recent work emphasizes that stars, in general, may have at least two distinct but very important centres: (I) a geometrical centre, and (II) a separate nuclear centre, residing in a shell outside a zero-luminosity dense core for example. This two-centre perspective leads to an explicit, analytical, asymptotic theory of low-mass red-giant structure. It enables one to appreciate that the problem of understanding why such stars become red giants is one of anticipating a remarkable yet natural structural bifurcation that occurs in them. This bifurcation occurs because of a combination of known and understandable facts just summarized namely that, following central hydrogen exhaustion, a thin nuclear-burning shell does develop outside a more-or-less dense core. In the resulting theory, both ρsh/ρolinec and ρsh·ρolinec prove to be important self-consistently derived quantities. I present some striking, explicit, asymptotic analytical theorems and results involving these quantities. Perhaps the most astonishingly unexpected and gratifying single result is this: for the very value Nature gives us for the relevant temperature exponent (η=15; CNO cycle) for nuclear-energy generation, ρsh and ρolinec behave in a well defined, precisely inverse manner for a given value of core-mass, Mc. This emphasizes that the internal behaviour of such stars is definitely anti-homologous rather than homologous: dense cores physically promote diffuse surrounding envelopes. I also extend the ideas yet further in a way which (I) links the structural and evolutionary behaviour of stars from the main sequence through horizontal-branch phases of evolution, and (II) also has implications for post-main-sequence developments in more massive stars. The end results is that the post-main-sequence developments of all stars - low-mass, intermediate-mass, and high-mass - as they expand to become giants, are finally seen to be examples of one underpinning fact: that dense cores with this surrounding shells naturally follow hydrogen exhaustion. While "this has been know all along" from oft-repeated computer calculations, we now know why analytically. That matters to true theorists. What follows is a requested, much expanded version of my Cambridge talk.

Sequence variation and phylogenetic analysis of envelope glycoprotein of hepatitis G virus.

PubMed

Lim, M Y; Fry, K; Yun, A; Chong, S; Linnen, J; Fung, K; Kim, J P

1997-11-01

A transfusion-transmissible agent provisionally designated hepatitis G virus (HGV) was recently identified. In this study, we examined the variability of the HGV genome by analysing sequences in the putative envelope region from 72 isolates obtained from diverse geographical sources. The 1561 nucleotide sequence of the E1/E2/NS2a region of HGV was determined from 12 isolates, and compared with three published sequences. The most variability was observed in 400 nucleotides at the N terminus of E2. We next analysed this 400 nucleotide envelope variable region (EV) from an additional 60 HGV isolates. This sequence varied considerably among the 75 isolates, with overall identity ranging from 79.3% to 99.5% at the nucleotide level, and from 83.5% to 100% at the amino acid level. However, hypervariable regions were not identified. Phylogenetic analyses indicated that the 75 HGV isolates belong to a single genotype. A single-tier distribution of evolutionary distances was observed among the 15 E1/E2/NS2a sequences and the 75 EV sequences. In contrast, 11 isolates of HCV were analysed and showed a three-tiered distribution, representing genotypes, subtypes, and isolates. The 75 isolates of HGV fell into four clusters on the phylogenetic tree. Tight geographical clustering was observed among the HGV isolates from Japan and Korea.

The Summerville Formation: Evidence for a sub-horizontal stratigraphic sequence below the post-rift unconformity in the Middleton Place Summerville Seismic Zone

NASA Astrophysics Data System (ADS)

Getz, Joseph Edward

The Middleton Place Summerville Seismic Zone (MPSSZ) near Summerville, South Carolina was the site of renewed extensive investigation, beginning in the 1970's, for the source of the 1886 Charleston earthquake. Reactivation of faults associated with a putative fault-bounded Triassic rift basin through analysis of seismic reflection, seismic refraction, and well data has since become the favored interpretation for the source of MPSSZ seismicity. Critical to this interpretation is the association of continental redbed sedimentary rocks with Triassic basins identified throughout the North American Atlantic margin. Reanalysis of 18 seismic reflection profiles and 25 seismic refraction profiles within the MPSSZ suggests that the red beds found here are a thin, sub-horizontal, regionally extensive, generally unbroken subsurface stratigraphic sequence distinct from the sedimentary architecture observed in analog Triassic rift systems. In addition, this sequence appears to unconformably overly a structural depression (the Jedberg basin) previously interpreted as a Triassic rift basin in the vicinity of the MPSSZ. In addition to the geometries observed on seismic reflection profiles, seismic refraction velocities ranging from 4.2 to 6.1 km/s can be correlated with (1) Jurassic basalt flows, (2) the newly proposed Summerville Formation, and (3) the Basement (B) sequences respectively. The current study maps the Summerville red bed section and its bounding reflectors. In addition to mapping the regional extent of the newly proposed Summerville Formation, refraction velocities and changes in reflection character, the lateral extent of the basalt flows can be changed to a more localized flow rather than a regionally extensive flow of which was previously thought. Reanalysis of data in the MPSSZ suggests that the area may not be part of the Triassic South Georgia Rift system due to the sub-horizontal geometry of the red bed reflections, the apparent lack of faulting, and their regional extent.

Genome-wide association study using high-density single nucleotide polymorphism arrays and whole-genome sequences for clinical mastitis traits in dairy cattle.

PubMed

Sahana, G; Guldbrandtsen, B; Thomsen, B; Holm, L-E; Panitz, F; Brøndum, R F; Bendixen, C; Lund, M S

2014-11-01

Mastitis is a mammary disease that frequently affects dairy cattle. Despite considerable research on the development of effective prevention and treatment strategies, mastitis continues to be a significant issue in bovine veterinary medicine. To identify major genes that affect mastitis in dairy cattle, 6 chromosomal regions on Bos taurus autosome (BTA) 6, 13, 16, 19, and 20 were selected from a genome scan for 9 mastitis phenotypes using imputed high-density single nucleotide polymorphism arrays. Association analyses using sequence-level variants for the 6 targeted regions were carried out to map causal variants using whole-genome sequence data from 3 breeds. The quantitative trait loci (QTL) discovery population comprised 4,992 progeny-tested Holstein bulls, and QTL were confirmed in 4,442 Nordic Red and 1,126 Jersey cattle. The targeted regions were imputed to the sequence level. The highest association signal for clinical mastitis was observed on BTA 6 at 88.97 Mb in Holstein cattle and was confirmed in Nordic Red cattle. The peak association region on BTA 6 contained 2 genes: vitamin D-binding protein precursor (GC) and neuropeptide FF receptor 2 (NPFFR2), which, based on known biological functions, are good candidates for affecting mastitis. However, strong linkage disequilibrium in this region prevented conclusive determination of the causal gene. A different QTL on BTA 6 located at 88.32 Mb in Holstein cattle affected mastitis. In addition, QTL on BTA 13 and 19 were confirmed to segregate in Nordic Red cattle and QTL on BTA 16 and 20 were confirmed in Jersey cattle. Although several candidate genes were identified in these targeted regions, it was not possible to identify a gene or polymorphism as the causal factor for any of these regions. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Organization and variation analysis of 5S rDNA in different ploidy-level hybrids of red crucian carp × topmouth culter.

PubMed

He, Weiguo; Qin, Qinbo; Liu, Shaojun; Li, Tangluo; Wang, Jing; Xiao, Jun; Xie, Lihua; Zhang, Chun; Liu, Yun

2012-01-01

Through distant crossing, diploid, triploid and tetraploid hybrids of red crucian carp (Carassius auratus red var., RCC♀, Cyprininae, 2n = 100) × topmouth culter (Erythroculter ilishaeformis Bleeker, TC♂, Cultrinae, 2n = 48) were successfully produced. Diploid hybrids possessed 74 chromosomes with one set from RCC and one set from TC; triploid hybrids harbored 124 chromosomes with two sets from RCC and one set from TC; tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from TC. The 5S rDNA of the three different ploidy-level hybrids and their parents were sequenced and analyzed. There were three monomeric 5S rDNA classes (designated class I: 203 bp; class II: 340 bp; and class III: 477 bp) in RCC and two monomeric 5S rDNA classes (designated class IV: 188 bp, and class V: 286 bp) in TC. In the hybrid offspring, diploid hybrids inherited three 5S rDNA classes from their female parent (RCC) and only class IV from their male parent (TC). Triploid hybrids inherited class II and class III from their female parent (RCC) and class IV from their male parent (TC). Tetraploid hybrids gained class II and class III from their female parent (RCC), and generated a new 5S rDNA sequence (designated class I-N). The specific paternal 5S rDNA sequence of class V was not found in the hybrid offspring. Sequence analysis of 5S rDNA revealed the influence of hybridization and polyploidization on the organization and variation of 5S rDNA in fish. This is the first report on the coexistence in vertebrates of viable diploid, triploid and tetraploid hybrids produced by crossing parents with different chromosome numbers, and these new hybrids are novel specimens for studying the genomic variation in the first generation of interspecific hybrids, which has significance for evolution and fish genetics.

Impact of commercial precooking of common bean (Phaseolus vulgaris) on the generation of peptides, after pepsin-pancreatin hydrolysis, capable to inhibit dipeptidyl peptidase-IV.

PubMed

Mojica, Luis; Chen, Karen; de Mejía, Elvira González

2015-01-01

The objective of this research was to determine the bioactive properties of the released peptides from commercially available precook common beans (Phaseolus vulgaris). Bioactive properties and peptide profiles were evaluated in protein hydrolysates of raw and commercially precooked common beans. Five varieties (Black, Pinto, Red, Navy, and Great Northern) were selected for protein extraction, protein and peptide molecular mass profiles, and peptide sequences. Potential bioactivities of hydrolysates, including antioxidant capacity and inhibition of α-amylase, α-glucosidase, dipeptidyl peptidase-IV (DPP-IV), and angiotensin converting enzyme I (ACE) were analyzed after digestion with pepsin/pancreatin. Hydrolysates from Navy beans were the most potent inhibitors of DPP-IV with no statistical differences between precooked and raw (IC50 = 0.093 and 0.095 mg protein/mL, respectively). α-Amylase inhibition was higher for raw Red, Navy and Great Northern beans (36%, 31%, 27% relative to acarbose (rel ac)/mg protein, respectively). α-Glucosidase inhibition among all bean hydrolysates did not show significant differences; however, inhibition values were above 40% rel ac/mg protein. IC50 values for ACE were not significantly different among all bean hydrolysates (range 0.20 to 0.34 mg protein/mL), except for Red bean that presented higher IC50 values. Peptide molecular mass profile ranged from 500 to 3000 Da. A total of 11 and 17 biologically active peptide sequences were identified in raw and precooked beans, respectively. Peptide sequences YAGGS and YAAGS from raw Great Northern and precooked Pinto showed similar amino acid sequences and same potential ACE inhibition activity. Processing did not affect the bioactive properties of released peptides from precooked beans. Commercially precooked beans could contribute to the intake of bioactive peptides and promote health. © 2014 Institute of Food Technologists®

A comparison of coding sequence and cytogenetic localization of the myostatin gene in the dog, red fox, arctic fox and Chinese raccoon dog.

PubMed

Grzes, M; Nowacka-Woszuk, J; Szczerbal, I; Czerwinska, J; Gracz, J; Switonski, M

2009-01-01

The gene encoding myostatin (MSTN), due to its crucial function for growth of skeletal muscle mass, is an important candidate for muscularity. In this study we analyzed the nucleotide sequence and FISH localization of this gene in 4 canids, including 3 farm species. The nucleotide sequence of the MSTN coding fragment turned out to be highly conserved, since its identity among the studied species was very high and varied between 99.4 and 99.7%. Only 1, widely spread, silent single nucleotide polymorphism (SNP) was found in exon 1 of the Chinese raccoon dog. The MSTN gene was localized close to the centromere in one-armed chromosomes of the dog (37q11) and bi-armed chromosomes of the red fox (16p11) and arctic fox (10q11), with an exception of the Chinese raccoon dog chromosome (2q14-q21). This chromosome is orthologous to 3 canine chromosomes and thus the MSTN was found more interstitially. Our results are in agreement with the hypothesis that karyotypes of the canids evolved mainly through centric fusion/fission events, while tandem fusions occurred rarely. (c) 2009 S. Karger AG, Basel.

Next-Generation Sequencing of an 88-Year-Old Specimen of the Poorly Known Species Liagora japonica (Nemaliales, Rhodophyta) Supports the Recognition of Otohimella gen. nov.

PubMed Central

Suzuki, Masahiro; Segawa, Takahiro; Mori, Hiroshi; Akiyoshi, Ayumi; Ootsuki, Ryo; Kurihara, Akira; Sakayama, Hidetoshi; Kitayama, Taiju; Abe, Tsuyoshi; Kogame, Kazuhiro; Kawai, Hiroshi; Nozaki, Hisayoshi

2016-01-01

Liagora japonica is a red algal species distributed in temperate regions of Japan. This species has not been collected from its type locality on the Pacific coast of Japan since 1927 and seems to have become extinct in this area. For molecular characterization of L. japonica, we extracted DNA from the topotype material of L. japonica collected in 1927, analyzed seven genes using Illumina next-generation sequencing, and compared these data with sequences from modern samples of similar red algae collected from the Japan Sea coast of Japan. Both morphological and molecular data from modern samples and historical specimens (including the lectotype and topotype) suggest that the specimens from the Pacific and Japan Sea coasts of Japan should be treated as a single species, and that L. japonica is phylogenetically separated from the genus Liagora. Based on the phylogenetic results and examination of reproductive structures, we propose Otohimella japonica gen. et comb. nov., characterized morphologically by diffuse carposporophytes, undivided carposporangia, and involucral filaments initiated only from the cortical cell on the supporting cell. PMID:27388436

Progressive Loss of Function in a Limb Enhancer during Snake Evolution.

PubMed

Kvon, Evgeny Z; Kamneva, Olga K; Melo, Uirá S; Barozzi, Iros; Osterwalder, Marco; Mannion, Brandon J; Tissières, Virginie; Pickle, Catherine S; Plajzer-Frick, Ingrid; Lee, Elizabeth A; Kato, Momoe; Garvin, Tyler H; Akiyama, Jennifer A; Afzal, Veena; Lopez-Rios, Javier; Rubin, Edward M; Dickel, Diane E; Pennacchio, Len A; Visel, Axel

2016-10-20

The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP. Copyright © 2016 Elsevier Inc. All rights reserved.

Investigation of Outbreaks of Salmonella enterica Serovar Typhimurium and Its Monophasic Variants Using Whole-Genome Sequencing, Denmark

PubMed Central

Gymoese, Pernille; Sørensen, Gitte; Litrup, Eva; Olsen, John Elmerdal; Nielsen, Eva Møller

2017-01-01

Whole-genome sequencing is rapidly replacing current molecular typing methods for surveillance purposes. Our study evaluates core-genome single-nucleotide polymorphism analysis for outbreak detection and linking of sources of Salmonella enterica serovar Typhimurium and its monophasic variants during a 7-month surveillance period in Denmark. We reanalyzed and defined 8 previously characterized outbreaks from the phylogenetic relatedness of the isolates, epidemiologic data, and food traceback investigations. All outbreaks were identified, and we were able to exclude unrelated and include additional related human cases. We were furthermore able to link possible food and veterinary sources to the outbreaks. Isolates clustered according to sequence types (STs) 19, 34, and 36. Our study shows that core-genome single-nucleotide polymorphism analysis is suitable for surveillance and outbreak investigation for Salmonella Typhimurium (ST19 and ST36), but whole genome–wide analysis may be required for the tight genetic clone of monophasic variants (ST34). PMID:28930002

A Photometric redshift galaxy catalog from the Red-Sequence Cluster Survey

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

Hsieh, Bau-Ching; /Taiwan, Natl. Central U. /Taipei, Inst. Astron. Astrophys.; Yee, H.K.C.

2005-02-01

The Red-Sequence Cluster Survey (RCS) provides a large and deep photometric catalog of galaxies in the z' and R{sub c} bands for 90 square degrees of sky, and supplemental V and B data have been obtained for 33.6 deg{sup 2}. They compile a photometric redshift catalog from these 4-band data by utilizing the empirical quadratic polynomial photometric redshift fitting technique in combination with CNOC2 and GOODS/HDF-N redshift data. The training set includes 4924 spectral redshifts. The resulting catalog contains more than one million galaxies with photometric redshifts < 1.5 and R{sub c} < 24, giving an rms scatter {delta}({Delta}z)

Margalef's mandala and phytoplankton bloom strategies

NASA Astrophysics Data System (ADS)

Wyatt, Timothy

2014-03-01

Margalef's mandala maps phytoplankton species into a phase space defined by turbulence (A) and nutrient concentrations (Ni); these are the hard axes. The permutations of high and low A and high and low Ni divide the space into four domains. Soft axes indicate some ecological dynamics. A main sequence shows the normal course of phytoplankton succession; the r-K axis of MacArthur and Wilson runs parallel to it. An alternative successional sequence leads to the low A-high Ni domain into which many red tide species are mapped. Astronomical and biological time are implicit. A mathematical transformation of the mandala (rotation) links it to the classical bloom models of Sverdrup (time) and Kierstead and Slobodkin (space). Both rarity and the propensity to form red tides are considered to be species characters, meaning that maximum population abundance can be a target of natural selection. Equally, both the unpredictable appearance of bloom species and their short-lived appearances may be species characters. There may be a correlation too between these features and long-lived dormant stages in the life-cycle; then the vegetative planktonic phase is the 'weak link' in the life-cycle. Red tides are thus due to species which have evolved suites of traits which result in specific demographic strategies.

Photosystem II Photochemistry and Phycobiliprotein of the Red Algae Kappaphycus alvarezii and Their Implications for Light Adaptation

PubMed Central

Wang, Jinfeng; Zhu, Jianyi; Yao, Chunyan; Liu, Jianguo; Qin, Song; Jiang, Peng

2013-01-01

Photosystem II photochemistry and phycobiliprotein (PBP) genes of red algae Kappaphycus alvarezii, raw material of κ-carrageenan used in food and pharmaceutical industries, were analyzed in this study. Minimum saturating irradiance (I k) of this algal species was less than 115 μmol m−2 s−1. Its actual PSII efficiency (yield II) increased when light intensity enhanced and decreased when light intensity reached 200 μmol m−2 s−1. Under dim light, yield II declined at first and then increased on the fourth day. Under high light, yield II retained a stable value. These results indicate that K. alvarezii is a low-light-adapted species but possesses regulative mechanisms in response to both excessive and deficient light. Based on the PBP gene sequences, K. alvarezii, together with other red algae, assembled faster and showed a closer relationship with LL-Prochlorococcus compared to HL-Prochlorococcus. Many amino acid loci in PBP sequences of K. alvarezii were conserved with those of LL-Prochlorococcus. However, loci conserved with HL-Prochlorococcus but divergent with LL-Prochlorococcus were also found. The diversities of PE and PC are proposed to have played some roles during the algal evolution and divergence of light adaption. PMID:24380080

Photosystem II photochemistry and phycobiliprotein of the red algae Kappaphycus alvarezii and their implications for light adaptation.

PubMed

Guan, Xiangyu; Wang, Jinfeng; Zhu, Jianyi; Yao, Chunyan; Liu, Jianguo; Qin, Song; Jiang, Peng

2013-01-01

Photosystem II photochemistry and phycobiliprotein (PBP) genes of red algae Kappaphycus alvarezii, raw material of κ -carrageenan used in food and pharmaceutical industries, were analyzed in this study. Minimum saturating irradiance (I k) of this algal species was less than 115 μmol m(-2) s(-1). Its actual PSII efficiency (yield II) increased when light intensity enhanced and decreased when light intensity reached 200 μmol m(-2) s(-1). Under dim light, yield II declined at first and then increased on the fourth day. Under high light, yield II retained a stable value. These results indicate that K. alvarezii is a low-light-adapted species but possesses regulative mechanisms in response to both excessive and deficient light. Based on the PBP gene sequences, K. alvarezii, together with other red algae, assembled faster and showed a closer relationship with LL-Prochlorococcus compared to HL-Prochlorococcus. Many amino acid loci in PBP sequences of K. alvarezii were conserved with those of LL-Prochlorococcus. However, loci conserved with HL-Prochlorococcus but divergent with LL-Prochlorococcus were also found. The diversities of PE and PC are proposed to have played some roles during the algal evolution and divergence of light adaption.

Transfers of stimulus function during roulette wagering.

PubMed

Dixon, Mark R; Enoch, Mary Rachel; Belisle, Jordan

2017-10-01

Twenty-five recreational gamblers were initially asked to place bets on either red or black positions on a roulette board in a simulated casino setting. Each participant was then exposed to a stimulus pairing observing procedure which attempted to develop equivalence classes between one color (black or red) and traditionally positive words (e.g., love, happy, sex) and another color (black or red) and traditionally negative words (e.g., death, cancer, taxes), in the absence of consequence manipulations. Twenty-one of the twenty-five participants demonstrated greater response allocation to the color position on the roulette board that participated in a relational network with the positive words. Variations in sequencing of experimental conditions had no impact on poststimulus-pairing wagers, but did impact tests for equivalence accuracy. © 2017 Society for the Experimental Analysis of Behavior.

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

PubMed Central

Thurber, Mary I.; Ghai, Ria R.; Hyeroba, Hyeroba; 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.

2013-01-01

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. PMID:23603520

A novel type of light-harvesting antenna protein of red algal origin in algae with secondary plastids.

PubMed

Sturm, Sabine; Engelken, Johannes; Gruber, Ansgar; Vugrinec, Sascha; Kroth, Peter G; Adamska, Iwona; Lavaud, Johann

2013-07-30

Light, the driving force of photosynthesis, can be harmful when present in excess; therefore, any light harvesting system requires photoprotection. Members of the extended light-harvesting complex (LHC) protein superfamily are involved in light harvesting as well as in photoprotection and are found in the red and green plant lineages, with a complex distribution pattern of subfamilies in the different algal lineages. Here, we demonstrate that the recently discovered "red lineage chlorophyll a/b-binding-like proteins" (RedCAPs) form a monophyletic family within this protein superfamily. The occurrence of RedCAPs was found to be restricted to the red algal lineage, including red algae (with primary plastids) as well as cryptophytes, haptophytes and heterokontophytes (with secondary plastids of red algal origin). Expression of a full-length RedCAP:GFP fusion construct in the diatom Phaeodactylum tricornutum confirmed the predicted plastid localisation of RedCAPs. Furthermore, we observed that similarly to the fucoxanthin chlorophyll a/c-binding light-harvesting antenna proteins also RedCAP transcripts in diatoms were regulated in a diurnal way at standard light conditions and strongly repressed at high light intensities. The absence of RedCAPs from the green lineage implies that RedCAPs evolved in the red lineage after separation from the the green lineage. During the evolution of secondary plastids, RedCAP genes therefore must have been transferred from the nucleus of the endocytobiotic alga to the nucleus of the host cell, a process that involved complementation with pre-sequences allowing import of the gene product into the secondary plastid bound by four membranes. Based on light-dependent transcription and on localisation data, we propose that RedCAPs might participate in the light (intensity and quality)-dependent structural or functional reorganisation of the light-harvesting antennae of the photosystems upon dark to light shifts as regularly experienced by diatoms in nature. Remarkably, in plastids of the red lineage as well as in green lineage plastids, the phycobilisome based cyanobacterial light harvesting system has been replaced by light harvesting systems that are based on members of the extended LHC protein superfamily, either for one of the photosystems (PS I of red algae) or for both (diatoms). In their proposed function, the RedCAP protein family may thus have played a role in the evolutionary structural remodelling of light-harvesting antennae in the red lineage.

A Flavin Binding Cryptochrome Photoreceptor Responds to Both Blue and Red Light in Chlamydomonas reinhardtii[W

PubMed Central

Beel, Benedikt; Prager, Katja; Spexard, Meike; Sasso, Severin; Weiss, Daniel; Müller, Nico; Heinnickel, Mark; Dewez, David; Ikoma, Danielle; Grossman, Arthur R.; Kottke, Tilman; Mittag, Maria

2012-01-01

Cryptochromes are flavoproteins that act as sensory blue light receptors in insects, plants, fungi, and bacteria. We have investigated a cryptochrome from the green alga Chlamydomonas reinhardtii with sequence homology to animal cryptochromes and (6-4) photolyases. In response to blue and red light exposure, this animal-like cryptochrome (aCRY) alters the light-dependent expression of various genes encoding proteins involved in chlorophyll and carotenoid biosynthesis, light-harvesting complexes, nitrogen metabolism, cell cycle control, and the circadian clock. Additionally, exposure to yellow but not far-red light leads to comparable increases in the expression of specific genes; this expression is significantly reduced in an acry insertional mutant. These in vivo effects are congruent with in vitro data showing that blue, yellow, and red light, but not far-red light, are absorbed by the neutral radical state of flavin in aCRY. The aCRY neutral radical is formed following blue light absorption of the oxidized flavin. Red illumination leads to conversion to the fully reduced state. Our data suggest that aCRY is a functionally important blue and red light–activated flavoprotein. The broad spectral response implies that the neutral radical state functions as a dark form in aCRY and expands the paradigm of flavoproteins and cryptochromes as blue light sensors to include other light qualities. PMID:22773746

Molecular and Ecological Evidence for Species Specificity and Coevolution in a Group of Marine Algal-Bacterial Symbioses

PubMed Central

Ashen, Jon B.; Goff, Lynda J.

2000-01-01

The phylogenetic relationships of bacterial symbionts from three gall-bearing species in the marine red algal genus Prionitis (Rhodophyta) were inferred from 16S rDNA sequence analysis and compared to host phylogeny also inferred from sequence comparisons (nuclear ribosomal internal-transcribed-spacer region). Gall formation has been described previously on two species of Prionitis, P. lanceolata (from central California) and P. decipiens (from Peru). This investigation reports gall formation on a third related host, Prionitis filiformis. Phylogenetic analyses based on sequence comparisons place the bacteria as a single lineage within the Roseobacter grouping of the α subclass of the division Proteobacteria (99.4 to 98.25% sequence identity among phylotypes). Comparison of symbiont and host molecular phylogenies confirms the presence of three gall-bearing algal lineages and is consistent with the hypothesis that these red seaweeds and their bacterial symbionts are coevolving. The species specificity of these associations was investigated in nature by whole-cell hybridization of gall bacteria and in the laboratory by using cross-inoculation trials. Whole-cell in situ hybridization confirmed that a single bacterial symbiont phylotype is present in galls on each host. In laboratory trials, bacterial symbionts were incapable of inducing galls on alternate hosts (including two non-gall-bearing species). Symbiont-host specificity in Prionitis gall formation indicates an effective ecological separation between these closely related symbiont phylotypes and provides an example of a biological context in which to consider the organismic significance of 16S rDNA sequence variation. PMID:10877801

Light-modulated abundance of an mRNA encoding a calmodulin-regulated, chromatin-associated NTPase in pea

NASA Technical Reports Server (NTRS)

Hsieh, H. L.; Tong, C. G.; Thomas, C.; Roux, S. J.

1996-01-01

A CDNA encoding a 47 kDa nucleoside triphosphatase (NTPase) that is associated with the chromatin of pea nuclei has been cloned and sequenced. The translated sequence of the cDNA includes several domains predicted by known biochemical properties of the enzyme, including five motifs characteristic of the ATP-binding domain of many proteins, several potential casein kinase II phosphorylation sites, a helix-turn-helix region characteristic of DNA-binding proteins, and a potential calmodulin-binding domain. The deduced primary structure also includes an N-terminal sequence that is a predicted signal peptide and an internal sequence that could serve as a bipartite-type nuclear localization signal. Both in situ immunocytochemistry of pea plumules and immunoblots of purified cell fractions indicate that most of the immunodetectable NTPase is within the nucleus, a compartment proteins typically reach through nuclear pores rather than through the endoplasmic reticulum pathway. The translated sequence has some similarity to that of human lamin C, but not high enough to account for the earlier observation that IgG against human lamin C binds to the NTPase in immunoblots. Northern blot analysis shows that the NTPase MRNA is strongly expressed in etiolated plumules, but only poorly or not at all in the leaf and stem tissues of light-grown plants. Accumulation of NTPase mRNA in etiolated seedlings is stimulated by brief treatments with both red and far-red light, as is characteristic of very low-fluence phytochrome responses. Southern blotting with pea genomic DNA indicates the NTPase is likely to be encoded by a single gene.

Whole transcriptome analysis of the poultry red mite Dermanyssus gallinae (De Geer, 1778).

PubMed

Schicht, Sabine; Qi, Weihong; Poveda, Lucy; Strube, Christina

2014-03-01

SUMMARY Although the poultry red mite Dermanyssus gallinae (De Geer, 1778) is the major parasitic pest in poultry farming causing substantial economic losses every year, nucleotide data are rare in the public databases. Therefore, de novo sequencing covering the transcriptome of D. gallinae was carried out resulting in a dataset of 232 097 singletons and 42 130 contiguous sequences (contigs) which were subsequently clustered into 24 140 isogroups consisting of 35 788 isotigs. After removal of sequences possibly originating from bacteria or the chicken host, 267 464 sequences (231 657 singletons, 56 contigs and 35 751 isotigs) remained, of which 10·3% showed homology to proteins derived from other organisms. The most significant Blast top-hit species was the mite Metaseiulus occidentalis followed by the tick Ixodes scapularis. To gain functional knowledge of D. gallinae transcripts, sequences were mapped to Gene Ontology terms, Kyoto Encyclopedia of Gene and Genomes (KEGG) pathways and parsed to InterProScan. The transcriptome dataset provides new insights in general mite genetics and lays a foundation for future studies on stage-specific transcriptomics as well as genomic, proteomic, and metabolomic explorations and might provide new perspectives to control this parasitic mite by identifying possible drug targets or vaccine candidates. It is also worth noting that in different tested species of the class Arachnida no 28S rRNA was detectable in the rRNA profile, indicating that 28S rRNA might consists of two separate, hydrogen-bonded fragments, whose (heat-induced) disruption may led to co-migration with 18S rRNA.

Phenotypic and genetic analysis of the German Malus Germplasm Collection in terms of type 1 and type 2 red-fleshed apples.

PubMed

Würdig, Juliane; Flachowsky, Henryk; Höfer, Monika; Peil, Andreas; Eldin Ali, Mohammed Ali Mohammed Saad; Hanke, Magda-Viola

2014-07-10

Red fruit flesh is a desirable trait in apple breeding, because red-fleshed apples are a novelty and therefore considered to be more attractive to consumers and contain more health beneficial compounds. The red fruit flesh coloration is based on an increased level of cyanidin 3-galactoside, an anthocyanin whose biosynthesis is regulated by the MYB-type transcription factors MdMYB10 or MdMYB110a, respectively. A repeated segment in the MdMYB10 promoter allele R6 results in a gain-of-function mutation visible as red pigmentation of fruit skin and flesh and all vegetative tissues. Red-fleshed apple genotypes containing this R6 allele belong to the type 1 red-fleshed apple, which is known to be linked to some negative traits like astringent taste and internal flesh browning disorder. In type 2 red-fleshed apples the fruit flesh coloration is not inevitably linked with skin and leaf color. This red-fleshed apple phenotype, which is a result of increased expression of MdMYB110a, seems to be more useful for breeding, but it can be found rather seldom. In the present study 357 Malus accessions of the German Malus Germplasm Collection were evaluated for red fruit flesh coloration and the presence of the MdMYB10 R1 (not mutated) and R6 promoter alleles. Among them a total of 40 accessions were identified which contain the R6 allele. 37 accessions showed a red coloration of the fruit flesh. All these accessions belong to type 1 red-fleshed apple. No type 2 red-fleshed apple could be found. Three accessions with R6 allele had non-red-fleshed apples. 312 other non-red-fleshed accessions contained only the R1 allele. Five non-red-fleshed accessions contained a new promoter allele with an unexpected size of ~1 kbp. Sequencing of this allele detected the insertion of a non-autonomous apple transposon. Copyright © 2014 Elsevier B.V. All rights reserved.

Analysis of horizontal genetic transfer in red algae in the post-genomics age

PubMed Central

Chan, Cheong Xin; Bhattacharya, Debashish

2013-01-01

The recently published genome of the unicellular red alga Porphyridium purpureum revealed a gene-rich, intron-poor species, which is surprising for a free-living mesophile. Of the 8,355 predicted protein-coding regions, up to 773 (9.3%) were implicated in horizontal genetic transfer (HGT) events involving other prokaryote and eukaryote lineages. A much smaller number, up to 174 (2.1%) showed unambiguous evidence of vertical inheritance. Together with other red algal genomes, nearly all published in 2013, these data provide an excellent platform for studying diverse aspects of algal biology and evolution. This novel information will help investigators test existing hypotheses about the impact of endosymbiosis and HGT on algal evolution and enable comparative analysis within a more-refined, hypothesis-driven framework that extends beyond HGT. Here we explore the impacts of this infusion of red algal genome data on addressing questions regarding the complex nature of algal evolution and highlight the need for scalable phylogenomic approaches to handle the forthcoming deluge of sequence information. PMID:24475368

Dominant colonization and inheritance of Methylobacterium sp. strain OR01 on perilla plants.

PubMed

Mizuno, Masayuki; Yurimoto, Hiroya; Iguchi, Hiroyuki; Tani, Akio; Sakai, Yasuyoshi

2013-01-01

Pink-pigmented facultative methylotrophs (PPFMs) are major inhabitants of the phyllosphere. In a preceding study, we found that perilla plants harbor a dominant population of PPFMs on their leaves and seeds, and that the closest relative of PPFMs (Methylobacterium sp. strain OR01 as representative strain) isolated from red perilla seeds was M. fujisawaense DSM5686(T). In the present study, the specific interaction between red perilla and Methylobacterium species was investigated. All the PPFMs isolated from red perilla seeds harvested in the Ohara area of Kyoto, Japan in 2009, 2010, and 2011 and the PPFMs isolated from red perilla leaves planted at four geographically different places in Japan had 16S rRNA sequences identical to that of strain OR01. Direct transmission of PPFMs from seeds to leaves and the competitiveness of strain OR01 were confirmed. This report is the first step toward understanding the species-level specificity of the interaction between perilla plants and Methylobacterium species.

Interconversion of Anthozoa GFP-like fluorescent and non-fluorescent proteins by mutagenesis

PubMed Central

Bulina, Maria E; Chudakov, Dmitry M; Mudrik, Nikolay N; Lukyanov, Konstantin A

2002-01-01

Background Within the family of green fluorescent protein (GFP) homologs, one can mark two main groups, specifically, fluorescent proteins (FPs) and non-fluorescent or chromoproteins (CPs). Structural background of differences between FPs and CPs are poorly understood to date. Results Here, we applied site-directed and random mutagenesis in order to to transform CP into FP and vice versa. A purple chromoprotein asCP (asFP595) from Anemonia sulcata and a red fluorescent protein DsRed from Discosoma sp. were selected as representatives of CPs and FPs, respectively. For asCP, some substitutions at positions 148 and 165 (numbering in accordance to GFP) were found to dramatically increase quantum yield of red fluorescence. For DsRed, substitutions at positions 148, 165, 167, and 203 significantly decreased fluorescence intensity, so that the spectral characteristics of these mutants became more close to those of CPs. Finally, a practically non-fluorescent mutant DsRed-NF was generated. This mutant carried four amino acid substitutions, specifically, S148C, I165N, K167M, and S203A. DsRed-NF possessed a high extinction coefficient and an extremely low quantum yield (< 0.001). These spectral characteristics allow one to regard DsRed-NF as a true chromoprotein. Conclusions We located a novel point in asCP sequence (position 165) mutations at which can result in red fluorescence appearance. Probably, this finding could be applied onto other CPs to generate red and far-red fluorescent mutants. A possibility to transform an FP into CP was demonstrated. Key role of residues adjacent to chromophore's phenolic ring in fluorescent/non-fluorescent states determination was revealed. PMID:11972899

An RNAi-enhanced Logic Circuit for Cancer Specific Detection and Destruction

DTIC Science & Technology

2010-07-01

Bcl-2 family: mBax (Mus musculus), hBax ( Homo sapiens ), and its mutant hBax-S184A [4]. A plasmid containing the tested gene was transfected into HEK...the far-red fluorescent protein mKate to express the Gata3 mStaple. Intron- feature sequences – donor site, branch point, poly- pyrimidine tract, and...intron-exon junction. Among the donor and acceptor sequences found in literature our intron features were chosen according SplicePort [5], an

Cloacal Prolapse in Raptors: Review of 16 Cases.

PubMed

Dutton, Thomas A G; Forbes, Neil A; Carrasco, Daniel Calvo

2016-06-01

Sixteen cases of cloacal prolapse in raptors were reviewed in this study. Colonic prolapse was the most common presentation (56% of cases). Red-tailed hawks ( Buteo jamaicensis ) were overrepresented, comprising 66% of colonic prolapse cases. In cases of colonic prolapse, postsurgical stricture formation was a commonly identified complication after resection and anastomosis of the colon. A novel technique was used in 2 cases of colonic prolapse, in which sterile, semirigid rubber tubing was placed in the distal colon and removed per-cloaca at the end of the procedure; this facilitated a secure, fluid-tight anastomosis while maintaining sufficient intestinal lumen. Oviductal prolapse (31% of cases) was associated with the most guarded prognosis (40% treatment success). Cloacoliths were treated successfully in 2 birds (13% of cases) by minimally invasive per-cloacal manual removal.

Out of Balance—Systemic Iron Homeostasis in Iron-Related Disorders

PubMed Central

Steinbicker, Andrea U.; Muckenthaler, Martina U.

2013-01-01

Iron is an essential element in our daily diet. Most iron is required for the de novo synthesis of red blood cells, where it plays a critical role in oxygen binding to hemoglobin. Thus, iron deficiency causes anemia, a major public health burden worldwide. On the other extreme, iron accumulation in critical organs such as liver, heart, and pancreas causes organ dysfunction due to the generation of oxidative stress. Therefore, systemic iron levels must be tightly balanced. Here we focus on the regulatory role of the hepcidin/ferroportin circuitry as the major regulator of systemic iron homeostasis. We discuss how regulatory cues (e.g., iron, inflammation, or hypoxia) affect the hepcidin response and how impairment of the hepcidin/ferroportin regulatory system causes disorders of iron metabolism. PMID:23917168

Recent origin and semi-permeable species boundaries in the scleractinian coral genus Stylophora from the Red Sea.

PubMed

Arrigoni, Roberto; Benzoni, Francesca; Terraneo, Tullia I; Caragnano, Annalisa; Berumen, Michael L

2016-10-07

Reticulate evolution, introgressive hybridisation, and phenotypic plasticity have been documented in scleractinian corals and have challenged our ability to interpret speciation processes. Stylophora is a key model system in coral biology and physiology, but genetic analyses have revealed that cryptic lineages concealed by morphological stasis exist in the Stylophora pistillata species complex. The Red Sea represents a hotspot for Stylophora biodiversity with six morphospecies described, two of which are regionally endemic. We investigated Stylophora species boundaries from the Red Sea and the associated Symbiodinium by sequencing seven DNA loci. Stylophora morphospecies from the Red Sea were not resolved based on mitochondrial phylogenies and showed nuclear allele sharing. Low genetic differentiation, weak isolation, and strong gene flow were found among morphospecies although no signals of genetic recombination were evident among them. Stylophora mamillata harboured Symbiodinium clade C whereas the other two Stylophora morphospecies hosted either Symbiodinium clade A or C. These evolutionary patterns suggest that either gene exchange occurs through reticulate evolution or that multiple ecomorphs of a phenotypically plastic species occur in the Red Sea. The recent origin of the lineage leading to the Red Sea Stylophora may indicate an ongoing speciation driven by environmental changes and incomplete lineage sorting.

Mass loss from red giants - Results from ultraviolet spectroscopy

NASA Technical Reports Server (NTRS)

Linsky, J. L.

1985-01-01

New instrumentation in space, primarily the IUE spacecraft, has enabled the application of ultraviolet spectroscopic techniques to the determination of physical properties and reliable mass loss rates for red giant winds. One important result is the determination of where in the H-R diagram are found stars with hot outer atmospheres and with cool winds. So far it appears that single cool stars, except perhaps the so-called hybrid stars, have either hot outer atmospheres or cool winds but not both. The C II resonance (1335 A) and intersystem (2325 A) multiplets have been used to derive temperatures, densities, and geometrical extents for the chromospheric portions of red giant winds, with the result that the red giants and the earlier giants with hot coronae have qualitatively different chromospheres. Mass loss rates can now be derived accurately from the analysis of asymmetric emission lines, such as the Mg II resonance lines, and from P Cygni profile lines of atoms in the dominant ionization stage when a hot star is available to probe the wind of a red giant. The Zeta Aur systems, consisting of a K-M supergiant and a main sequence B star are important systems for reliable mass loss rates for the red supergiant components are becoming available.

Recent origin and semi-permeable species boundaries in the scleractinian coral genus Stylophora from the Red Sea

PubMed Central

Arrigoni, Roberto; Benzoni, Francesca; Terraneo, Tullia I.; Caragnano, Annalisa; Berumen, Michael L.

2016-01-01

Reticulate evolution, introgressive hybridisation, and phenotypic plasticity have been documented in scleractinian corals and have challenged our ability to interpret speciation processes. Stylophora is a key model system in coral biology and physiology, but genetic analyses have revealed that cryptic lineages concealed by morphological stasis exist in the Stylophora pistillata species complex. The Red Sea represents a hotspot for Stylophora biodiversity with six morphospecies described, two of which are regionally endemic. We investigated Stylophora species boundaries from the Red Sea and the associated Symbiodinium by sequencing seven DNA loci. Stylophora morphospecies from the Red Sea were not resolved based on mitochondrial phylogenies and showed nuclear allele sharing. Low genetic differentiation, weak isolation, and strong gene flow were found among morphospecies although no signals of genetic recombination were evident among them. Stylophora mamillata harboured Symbiodinium clade C whereas the other two Stylophora morphospecies hosted either Symbiodinium clade A or C. These evolutionary patterns suggest that either gene exchange occurs through reticulate evolution or that multiple ecomorphs of a phenotypically plastic species occur in the Red Sea. The recent origin of the lineage leading to the Red Sea Stylophora may indicate an ongoing speciation driven by environmental changes and incomplete lineage sorting. PMID:27713475

Peruvian Maca (Lepidium peruvianum) – III: The Effects of Cultivation Altitude on Phytochemical and Genetic Differences in the Four Prime Maca Phenotypes

PubMed Central

Meissner, Henry O.; Mscisz, Alina; Baraniak, Marek; Piatkowska, Ewa; Pisulewski, Pawel; Mrozikiewicz, Mieczyslaw; Bobkiewicz-Kozlowska, Teresa

2017-01-01

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. PMID:28824342

RCSLenS: The Red Cluster Sequence Lensing Survey

NASA Astrophysics Data System (ADS)

Hildebrandt, H.; Choi, A.; Heymans, C.; Blake, C.; Erben, T.; Miller, L.; Nakajima, R.; van Waerbeke, L.; Viola, M.; Buddendiek, A.; Harnois-Déraps, J.; Hojjati, A.; Joachimi, B.; Joudaki, S.; Kitching, T. D.; Wolf, C.; Gwyn, S.; Johnson, N.; Kuijken, K.; Sheikhbahaee, Z.; Tudorica, A.; Yee, H. K. C.

2016-11-01

We present the Red Cluster Sequence Lensing Survey (RCSLenS), an application of the methods developed for the Canada-France-Hawaii Telescope Lensing Survey (CFHTLenS) to the ˜785 deg2, multi-band imaging data of the Red-sequence Cluster Survey 2. This project represents the largest public, sub-arcsecond seeing, multi-band survey to date that is suited for weak gravitational lensing measurements. With a careful assessment of systematic errors in shape measurements and photometric redshifts, we extend the use of this data set to allow cross-correlation analyses between weak lensing observables and other data sets. We describe the imaging data, the data reduction, masking, multi-colour photometry, photometric redshifts, shape measurements, tests for systematic errors, and a blinding scheme to allow for more objective measurements. In total, we analyse 761 pointings with r-band coverage, which constitutes our lensing sample. Residual large-scale B-mode systematics prevent the use of this shear catalogue for cosmic shear science. The effective number density of lensing sources over an unmasked area of 571.7 deg2 and down to a magnitude limit of r ˜ 24.5 is 8.1 galaxies per arcmin2 (weighted: 5.5 arcmin-2) distributed over 14 patches on the sky. Photometric redshifts based on four-band griz data are available for 513 pointings covering an unmasked area of 383.5 deg2. We present weak lensing mass reconstructions of some example clusters as well as the full survey representing the largest areas that have been mapped in this way. All our data products are publicly available through Canadian Astronomy Data Centre at http://www.cadc-ccda.hia-iha.nrc-cnrc.gc.ca/en/community/rcslens/query.html in a format very similar to the CFHTLenS data release.

Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools.

PubMed

Guizard, Sébastien; Piégu, Benoît; Arensburger, Peter; Guillou, Florian; Bigot, Yves

2016-08-19

The program RepeatMasker and the database Repbase-ISB are part of the most widely used strategy for annotating repeats in animal genomes. They have been used to show that avian genomes have a lower repeat content (8-12 %) than the sequenced genomes of many vertebrate species (30-55 %). However, the efficiency of such a library-based strategies is dependent on the quality and completeness of the sequences in the database that is used. An alternative to these library based methods are methods that identify repeats de novo. These alternative methods have existed for a least a decade and may be more powerful than the library based methods. We have used an annotation strategy involving several complementary de novo tools to determine the repeat content of the model genome galGal4 (1.04 Gbp), including identifying simple sequence repeats (SSRs), tandem repeats and transposable elements (TEs). We annotated over one Gbp. of the galGal4 genome and showed that it is composed of approximately 19 % SSRs and TEs repeats. Furthermore, we estimate that the actual genome of the red jungle fowl contains about 31-35 % repeats. We find that library-based methods tend to overestimate TE diversity. These results have a major impact on the current understanding of repeats distributions throughout chromosomes in the red jungle fowl. Our results are a proof of concept of the reliability of using de novo tools to annotate repeats in large animal genomes. They have also revealed issues that will need to be resolved in order to develop gold-standard methodologies for annotating repeats in eukaryote genomes.

The empirical Gaia G-band extinction coefficient

NASA Astrophysics Data System (ADS)

Danielski, C.; Babusiaux, C.; Ruiz-Dern, L.; Sartoretti, P.; Arenou, F.

2018-06-01

Context. The first Gaia data release unlocked the access to photometric information for 1.1 billion sources in the G-band. Yet, given the high level of degeneracy between extinction and spectral energy distribution for large passbands such as the Gaia G-band, a correction for the interstellar reddening is needed in order to exploit Gaia data. Aims: The purpose of this manuscript is to provide the empirical estimation of the Gaia G-band extinction coefficient kG for both the red giants and main sequence stars in order to be able to exploit the first data release DR1. Methods: We selected two samples of single stars: one for the red giants and one for the main sequence. Both samples are the result of a cross-match between Gaia DR1 and 2MASS catalogues; they consist of high-quality photometry in the G-, J- and KS-bands. These samples were complemented by temperature and metallicity information retrieved from APOGEE DR13 and LAMOST DR2 surveys, respectively. We implemented a Markov chain Monte Carlo method where we used (G - KS)0 versus Teff and (J - KS)0 versus (G - KS)0, calibration relations to estimate the extinction coefficient kG and we quantify its corresponding confidence interval via bootstrap resampling. We tested our method on samples of red giants and main sequence stars, finding consistent solutions. Results: We present here the determination of the Gaia extinction coefficient through a completely empirical method. Furthermore we provide the scientific community with a formula for measuring the extinction coefficient as a function of stellar effective temperature, the intrinsic colour (G - KS)0, and absorption.

Identification and cloning of a type III polyketide synthase required for diffusible pigment biosynthesis in Saccharopolyspora erythraea.

PubMed

Cortés, Jesús; Velasco, Javier; Foster, Graham; Blackaby, Andrew P; Rudd, Brian A M; Wilkinson, Barrie

2002-06-01

The soluble, diffusible red-brown pigment produced by a Saccharopolyspora erythraea "red variant" has been shown to contain glycosylated and polymerized derivatives of 2,5,7-trihydroxy-1,4-naphthoquinone (flaviolin). Flaviolin is a spontaneous oxidation product of 1,3,6,8-tetrahydroxynaphthalene (THN), which is biosynthesized in bacteria by a chalcone synthase-like (CS-like) type III polyketide synthase (PKS). A fragment of the gene responsible for THN biosynthesis in S. erythraea E_8-7 was amplified by polymerase chain reaction (PCR) using degenerate primers based on conserved regions of known plant CS and bacterial CS-like genes. From the isolated fragment, a suicide vector was prepared, which was subsequently used to disrupt the red-brown pigment-producing (rpp) locus in S. erythraea, generating a mutant that displayed an albino phenotype. Chromosomal DNA from the albino mutant was subsequently used in a vector-recapture protocol to isolate a plasmid that contained an insert spanning the entire rpp locus. Sequencing of the insert revealed that the disrupted open reading frame (ORF) encodes a CS-like protein displaying 69% sequence identity to the rppA gene of Streptomyces griseus. The S. griseus rppA gene encodes RppA, the first characterized bacterial CS-like protein, which is sufficient in vitro for the synthesis of THN from malonyl-CoA. The rppA disruption mutant and rppA sequence provided a means by which to address the mechanism of diffusible pigment biosynthesis, as well as to investigate any link between this and the modulation of erythromycin A titre, which has been observed for S. erythraea variants.

Are algal genes in nonphotosynthetic protists evidence of historical plastid endosymbioses?

PubMed

Stiller, John W; Huang, Jinling; Ding, Qin; Tian, Jing; Goodwillie, Carol

2009-10-20

How photosynthetic organelles, or plastids, were acquired by diverse eukaryotes is among the most hotly debated topics in broad scale eukaryotic evolution. The history of plastid endosymbioses commonly is interpreted under the "chromalveolate" hypothesis, which requires numerous plastid losses from certain heterotrophic groups that now are entirely aplastidic. In this context, discoveries of putatively algal genes in plastid-lacking protists have been cited as evidence of gene transfer from a photosynthetic endosymbiont that subsequently was lost completely. Here we examine this evidence, as it pertains to the chromalveolate hypothesis, through genome-level statistical analyses of similarity scores from queries with two diatoms, Phaeodactylum tricornutum and Thalassiosira pseudonana, and two aplastidic sister taxa, Phytophthora ramorum and P. sojae. Contingency tests of specific predictions of the chromalveolate model find no evidence for an unusual red algal contribution to Phytophthora genomes, nor that putative cyanobacterial sequences that are present entered these genomes through a red algal endosymbiosis. Examination of genes unrelated to plastid function provide extraordinarily significant support for both of these predictions in diatoms, the control group where a red endosymbiosis is known to have occurred, but none of that support is present in genes specifically conserved between diatoms and oomycetes. In addition, we uncovered a strong association between overall sequence similarities among taxa and relative sizes of genomic data sets in numbers of genes. Signal from "algal" genes in oomycete genomes is inconsistent with the chromalveolate hypothesis, and better explained by alternative models of sequence and genome evolution. Combined with the numerous sources of intragenomic phylogenetic conflict characterized previously, our results underscore the potential to be mislead by a posteriori interpretations of variable phylogenetic signals contained in complex genome-level data. They argue strongly for explicit testing of the different a priori assumptions inherent in competing evolutionary hypotheses.

Microbial communities and organic biomarkers in a Proterozoic-analog sinkhole.

PubMed

Hamilton, T L; Welander, P V; Albrecht, H L; Fulton, J M; Schaperdoth, I; Bird, L R; Summons, R E; Freeman, K H; Macalady, J L

2017-11-01

Little Salt Spring (Sarasota County, FL, USA) is a sinkhole with groundwater vents at ~77 m depth. The entire water column experiences sulfidic (~50 μM) conditions seasonally, resulting in a system poised between oxic and sulfidic conditions. Red pinnacle mats occupy the sediment-water interface in the sunlit upper basin of the sinkhole, and yielded 16S rRNA gene clones affiliated with Cyanobacteria, Chlorobi, and sulfate-reducing clades of Deltaproteobacteria. Nine bacteriochlorophyll e homologues and isorenieratene indicate contributions from Chlorobi, and abundant chlorophyll a and pheophytin a are consistent with the presence of Cyanobacteria. The red pinnacle mat contains hopanoids, including 2-methyl structures that have been interpreted as biomarkers for Cyanobacteria. A single sequence of hpnP, the gene required for methylation of hopanoids at the C-2 position, was recovered in both DNA and cDNA libraries from the red pinnacle mat. The hpnP sequence was most closely related to cyanobacterial hpnP sequences, implying that Cyanobacteria are a source of 2-methyl hopanoids present in the mat. The mats are capable of light-dependent primary productivity as evidenced by 13 C-bicarbonate photoassimilation. We also observed 13 C-bicarbonate photoassimilation in the presence of DCMU, an inhibitor of electron transfer to Photosystem II. Our results indicate that the mats carry out light-driven primary production in the absence of oxygen production-a mechanism that may have delayed the oxygenation of the Earth's oceans and atmosphere during the Proterozoic Eon. Furthermore, our observations of the production of 2-methyl hopanoids by Cyanobacteria under conditions of low oxygen and low light are consistent with the recovery of these structures from ancient black shales as well as their paucity in modern marine environments. © 2017 The Authors. Geobiology Published by John Wiley & Sons Ltd.

The Afar Depression: Was There a Triple Junction Above the Mantle Plume?

NASA Astrophysics Data System (ADS)

Ebinger, C.; Wolfenden, E.; Yirgu, G.; Ayalew, D.; Eagles, G.; Gloaguen, R.; Tiberi, C.; Rowland, J. R.; Deino, A.; Tesfaye, A.; Tesfaye, S.

2002-12-01

The Red Sea - Gulf of Aden- Main Ethiopian rift systems (Afar Depression) have served as the textbook example of a R-R-R triple junction zone which formed above a mantle plume (Ethiopia-Yemen flood basalt province, 31-28 Ma). Recent work has documented the onset and propagation of seafloor along the length of the Gulf of Aden and Red Sea arms, but the timing of continental rifting had been poorly constrained. Our aims were to constrain the timing of rift initiation in each arm of the rift near the proposed Oligocene triple junction and to re-assess models for break-up above a mantle plume. Although much of the early history of rifting is deeply buried by Pliocene-Recent lavas, erosional dissection of the rift margins provides windows into the early rift history. Along the southernmost Red Sea, faults commonly marked by eruptive centers initiated at about 26 Ma, coincident with rifting along the easternmost Gulf of Aden. New data from the rift immediately south of the southernmost Red Sea basin (ca.10N) constrain the earliest rift sequences in the northern Main Ethiopian rift (MER). Field and Ar-Ar data from sequences overlying the pre-rift flood basalts show that extension in the northern MER commenced at 12-10 Ma when the two rift systems were finally linked. The active zone of extension and magmatism in the southern Red Sea and eastern Gulf of Aden, however, had migrated east and north, respectively. Summarising, rifting in southern Ethiopia had commenced by 16-18 Ma, and had propagated northward to cut across Oligo-Miocene rift structures of the Red Sea and Gulf of Aden by 10 Ma, consistent with plate kinematic data. A triple junction could have developed only during the past 10 My, long after flood basaltic magmatism. Inverse models of gravity data predict a significant step (2-4 km) in the Moho where the youthful, less extended MER breaks into the Afar Depression. Project EAGLE (UK-US-Ethiopia) is now acquiring seismic data across and along this zone to evaluate mechanisms for rift segmentation and propagation prior to breakup.

Strobe Traffic Lights Warn of Approaching Emergency Vehicles

NASA Technical Reports Server (NTRS)

Bachelder, Aaron

2004-01-01

Strobe-enhanced traffic signals have been developed to aid in the preemption of road intersections for emergency vehicles. The strobe-enhanced traffic signals can be incorporated into both new and pre-existing traffic-control systems in which the traffic-signal heads are of a relatively new type based on arrays of light-emitting diodes (LEDs). The strobe-enhanced traffic signals offer a less expensive, less complex alternative to a recently developed system of LED-based warning signs placed next to traffic signals. Because of its visual complexity, the combination of traffic signals and warning signs is potentially confusing to motorists. The strobe-enhanced traffic signals present less visual clutter. In a given traffic-signal head, the strobe-enhanced traffic signal is embedded in the red LED array of the stop signal. Two strobe LED strips one horizontal and one vertical are made capable of operating separately from the rest of the red LED matrix. When no emergency vehicle is approaching, the red LED array functions as a normal stop signal: all the red LEDs are turned on and off together. When the intersection is to be preempted for an approaching emergency vehicle, only the LEDs in one of the strobe strips are lit, and are turned on in a sequence that indicates the direction of approach. For example (see figure), if an emergency vehicle approaches from the right, the strobe LEDs are lit in a sequence moving from right to left. Important to the success of strobe-enhanced traffic signals is conformance to city ordinances and close relation to pre-existing traffic standards. For instance, one key restriction is that new icons must not include arrows, so that motorists will not confuse new icons with conventional arrows that indicate allowed directions of movement. It is also critical that new displays like strobe-enhanced traffic signals be similar to displays used in traffic-control systems in large cities. For example, Charleston, South Carolina uses horizontal strobes on red traffic lights to alert motorists and thereby help motorists not to miss red lights. The one significant potential disadvantage of strobe-enhanced traffic lights is initial unfamiliarity on the part of motorists.

Spatial and Temporal Strain Distribution Along the Central Red Sea Rift - A Study of the Hamd-Jizil Basin in Saudi Arabia

NASA Astrophysics Data System (ADS)

Szymanski, E.; Stockli, D.; Johnson, P.; Kattan, F. H.; Al Shamari, A.

2006-12-01

Numerous models exploring the rupturing modes and mechanisms of continental lithosphere are based on geological evidence from the Red Sea/Gulf of Suez rift system. Individually, the Red Sea basin is the prototype for many models of orthogonal continental rifting. Despite being a classic example of continental extension, many temporal and spatial strain distribution aspects, as well as the dynamic evolution of the rift architecture of the Red Sea, remain poorly constrained. Critical data come mostly from the Gulf of Suez and the Egyptian and Yemeni margins of the Red Sea; the rift flanks in Sudan and Saudi Arabia have remained largely unstudied, leaving a large information gap along the central portions of the rift system. Improving continental lithosphere rupture models requires an absolute understanding of the timing and magnitude of strain partitioning along the full rift flank. This study focuses on the development of extensional structures, syn- extensional sedimentary deposits, and rift-related Tertiary basaltic volcanism along the central flank of the rift system in Saudi Arabia. Geo- and thermochronometric techniques are used to elucidate the evolution of inboard and outboard strain markers manifested by structurally-controlled extensional basins that parallel the trend of the main Red Sea rift. Constraints on the dynamics of rift flank deformation are achieved through the collection of thermochronometric transects that traverse both the entire Arabian shield and individual normal faults that bound inland basins. Preliminary results show inland basins as asymmetric half-grabens filled by tilted Cenozoic sedimentary strata and separated by exhumed basement fault blocks. The most prominent extensional basin is the NW-trending Hamd-Jizil basin, located north of Madinah, measuring ~200 km along strike and up to 20 km in width. The Hamd-Jizil basin is structurally characterized by two half-grabens exposing a series of syn-rift siliciclastic sedimentary sections below Tertiary basalts. In certain areas, thick basalt sequences provide basin infill and appear faulted by a younger series of normal faults. Work continues on the production of further geo- and thermochronologic data for the Tertiary basalt sequences as well as the entire rift flank region.

ATNT: an enhanced system for expression of polycistronic secondary metabolite gene clusters in Aspergillus niger.

PubMed

Geib, Elena; Brock, Matthias

2017-01-01

Fungi are treasure chests for yet unexplored natural products. However, exploitation of their real potential remains difficult as a significant proportion of biosynthetic gene clusters appears silent under standard laboratory conditions. Therefore, elucidation of novel products requires gene activation or heterologous expression. For heterologous gene expression, we previously developed an expression platform in Aspergillus niger that is based on the transcriptional regulator TerR and its target promoter P terA . In this study, we extended this system by regulating expression of terR  by the doxycycline inducible Tet-on system. Reporter genes cloned under the control of the target promoter P terA remained silent in the absence of doxycycline, but were strongly expressed when doxycycline was added. Reporter quantification revealed that the coupled system results in about five times higher expression rates compared to gene expression under direct control of the Tet-on system. As production of secondary metabolites generally requires the expression of several biosynthetic genes, the suitability of the self-cleaving viral peptide sequence P2A was tested in this optimised expression system. P2A allowed polycistronic expression of genes required for Asp-melanin formation in combination with the gene coding for the red fluorescent protein tdTomato. Gene expression and Asp-melanin formation was prevented in the absence of doxycycline and strongly induced by addition of doxycycline. Fluorescence studies confirmed the correct subcellular localisation of the respective enzymes. This tightly regulated but strongly inducible expression system enables high level production of secondary metabolites most likely even those with toxic potential. Furthermore, this system is compatible with polycistronic gene expression and, thus, suitable for the discovery of novel natural products.

Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea

PubMed Central

Ionescu, Danny; Siebert, Christian; Polerecky, Lubos; Munwes, Yaniv Y.; Lott, Christian; Häusler, Stefan; Bižić-Ionescu, Mina; Quast, Christian; Peplies, Jörg; Glöckner, Frank Oliver; Ramette, Alban; Rödiger, Tino; Dittmar, Thorsten; Oren, Aharon; Geyer, Stefan; Stärk, Hans-Joachim; Sauter, Martin; Licha, Tobias; Laronne, Jonathan B.; de Beer, Dirk

2012-01-01

Due to its extreme salinity and high Mg concentration the Dead Sea is characterized by a very low density of cells most of which are Archaea. We discovered several underwater fresh to brackish water springs in the Dead Sea harboring dense microbial communities. We provide the first characterization of these communities, discuss their possible origin, hydrochemical environment, energetic resources and the putative biogeochemical pathways they are mediating. Pyrosequencing of the 16S rRNA gene and community fingerprinting methods showed that the spring community originates from the Dead Sea sediments and not from the aquifer. Furthermore, it suggested that there is a dense Archaeal community in the shoreline pore water of the lake. Sequences of bacterial sulfate reducers, nitrifiers iron oxidizers and iron reducers were identified as well. Analysis of white and green biofilms suggested that sulfide oxidation through chemolitotrophy and phototrophy is highly significant. Hyperspectral analysis showed a tight association between abundant green sulfur bacteria and cyanobacteria in the green biofilms. Together, our findings show that the Dead Sea floor harbors diverse microbial communities, part of which is not known from other hypersaline environments. Analysis of the water’s chemistry shows evidence of microbial activity along the path and suggests that the springs supply nitrogen, phosphorus and organic matter to the microbial communities in the Dead Sea. The underwater springs are a newly recognized water source for the Dead Sea. Their input of microorganisms and nutrients needs to be considered in the assessment of possible impact of dilution events of the lake surface waters, such as those that will occur in the future due to the intended establishment of the Red Sea−Dead Sea water conduit. PMID:22679498

High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic.

PubMed

Sealfon, Rachel; Gire, Stephen; Ellis, Crystal; Calderwood, Stephen; Qadri, Firdausi; Hensley, Lisa; Kellis, Manolis; Ryan, Edward T; LaRocque, Regina C; Harris, Jason B; Sabeti, Pardis C

2012-09-11

Whole-genome sequencing is an important tool for understanding microbial evolution and identifying the emergence of functionally important variants over the course of epidemics. In October 2010, a severe cholera epidemic began in Haiti, with additional cases identified in the neighboring Dominican Republic. We used whole-genome approaches to sequence four Vibrio cholerae isolates from Haiti and the Dominican Republic and three additional V. cholerae isolates to a high depth of coverage (>2000x); four of the seven isolates were previously sequenced. Using these sequence data, we examined the effect of depth of coverage and sequencing platform on genome assembly and identification of sequence variants. We found that 50x coverage is sufficient to construct a whole-genome assembly and to accurately call most variants from 100 base pair paired-end sequencing reads. Phylogenetic analysis between the newly sequenced and thirty-three previously sequenced V. cholerae isolates indicates that the Haitian and Dominican Republic isolates are closest to strains from South Asia. The Haitian and Dominican Republic isolates form a tight cluster, with only four variants unique to individual isolates. These variants are located in the CTX region, the SXT region, and the core genome. Of the 126 mutations identified that separate the Haiti-Dominican Republic cluster from the V. cholerae reference strain (N16961), 73 are non-synonymous changes, and a number of these changes cluster in specific genes and pathways. Sequence variant analyses of V. cholerae isolates, including multiple isolates from the Haitian outbreak, identify coverage-specific and technology-specific effects on variant detection, and provide insight into genomic change and functional evolution during an epidemic.

A clustering package for nucleotide sequences using Laplacian Eigenmaps and Gaussian Mixture Model.

PubMed

Bruneau, Marine; Mottet, Thierry; Moulin, Serge; Kerbiriou, Maël; Chouly, Franz; Chretien, Stéphane; Guyeux, Christophe

2018-02-01

In this article, a new Python package for nucleotide sequences clustering is proposed. This package, freely available on-line, implements a Laplacian eigenmap embedding and a Gaussian Mixture Model for DNA clustering. It takes nucleotide sequences as input, and produces the optimal number of clusters along with a relevant visualization. Despite the fact that we did not optimise the computational speed, our method still performs reasonably well in practice. Our focus was mainly on data analytics and accuracy and as a result, our approach outperforms the state of the art, even in the case of divergent sequences. Furthermore, an a priori knowledge on the number of clusters is not required here. For the sake of illustration, this method is applied on a set of 100 DNA sequences taken from the mitochondrially encoded NADH dehydrogenase 3 (ND3) gene, extracted from a collection of Platyhelminthes and Nematoda species. The resulting clusters are tightly consistent with the phylogenetic tree computed using a maximum likelihood approach on gene alignment. They are coherent too with the NCBI taxonomy. Further test results based on synthesized data are then provided, showing that the proposed approach is better able to recover the clusters than the most widely used software, namely Cd-hit-est and BLASTClust. Copyright © 2017 Elsevier Ltd. All rights reserved.

Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms

PubMed Central

Kameshwar, Ayyappa kumar Sista; Qin, Wensheng

2016-01-01

Lignin is a complex polyphenyl aromatic compound which exists in tight associations with cellulose and hemicellulose to form plant primary and secondary cell wall. Lignocellulose is an abundant renewable biomaterial present on the earth. It has gained much attention in the scientific community in recent years because of its potential applications in bio-based industries. Microbial degradation of lignocellulose polymers was well studied in wood decaying fungi. Based on the plant materials they degrade these fungi were classified as white rot, brown rot and soft rot. However, some groups of bacteria belonging to the actinomycetes, α-proteobacteria and β-proteobacteria were also found to be efficient in degrading lignocellulosic biomass but not well understood unlike the fungi. In this review we focus on recent advancements deployed for finding and understanding the lignocellulose degradation by microorganisms. Conventional molecular methods like sequencing 16s rRNA and Inter Transcribed Spacer (ITS) regions were used for identification and classification of microbes. Recent progression in genomics mainly next generation sequencing technologies made the whole genome sequencing of microbes possible in a great ease. The whole genome sequence studies reveals high quality information about genes and canonical pathways involved in the lignin and other cell wall components degradation. PMID:26884714

Mitochondrial Intronic Open Reading Frames in Podospora: Mobility and Consecutive Exonic Sequence Variations

PubMed Central

Sellem, C. H.; d'Aubenton-Carafa, Y.; Rossignol, M.; Belcour, L.

1996-01-01

The mitochondrial genome of 23 wild-type strains belonging to three different species of the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group I intronic ORFs are mobile elements and that their transfer, and comcomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes. PMID:8725226

Mitochondrial intronic open reading frames in Podospora: mobility and consecutive exonic sequence variations.

PubMed

Sellem, C H; d'Aubenton-Carafa, Y; Rossignol, M; Belcour, L

1996-06-01

The mitochondrial genome of 23 wild-type strains belonging to three different species of the filamentous fungus Podospora was examined. Among the 15 optional sequences identified are two intronic reading frames, nad1-i4-orf1 and cox1-i7-orf2. We show that the presence of these sequences was strictly correlated with tightly clustered nucleotide substitutions in the adjacent exon. This correlation applies to the presence or absence of closely related open reading frames (ORFs), found at the same genetic locations, in all the Pyrenomycete genera examined. The recent gain of these optional ORFs in the evolution of the genus Podospora probably account for such sequence differences. In the homoplasmic progeny from heteroplasmons constructed between Podospora strains differing by the presence of these optional ORFs, nad1-i4-orf1 and cox1-i7-orf2 appeared highly invasive. Sequence comparisons in the nad1-i4 intron of various strains of the Pyrenomycete family led us to propose a scenario of its evolution that includes several events of loss and gain of intronic ORFs. These results strongly reinforce the idea that group 1 intronic ORFs are mobile elements and that their transfer, and concomitant modification of the adjacent exon, could participate in the modular evolution of mitochondrial genomes.

The sequence of camelpox virus shows it is most closely related to variola virus, the cause of smallpox.

PubMed

Gubser, Caroline; Smith, Geoffrey L

2002-04-01

Camelpox virus (CMPV) and variola virus (VAR) are orthopoxviruses (OPVs) that share several biological features and cause high mortality and morbidity in their single host species. The sequence of a virulent CMPV strain was determined; it is 202182 bp long, with inverted terminal repeats (ITRs) of 6045 bp and has 206 predicted open reading frames (ORFs). As for other poxviruses, the genes are tightly packed with little non-coding sequence. Most genes within 25 kb of each terminus are transcribed outwards towards the terminus, whereas genes within the centre of the genome are transcribed from either DNA strand. The central region of the genome contains genes that are highly conserved in other OPVs and 87 of these are conserved in all sequenced chordopoxviruses. In contrast, genes towards either terminus are more variable and encode proteins involved in host range, virulence or immunomodulation. In some cases, these are broken versions of genes found in other OPVs. The relationship of CMPV to other OPVs was analysed by comparisons of DNA and predicted protein sequences, repeats within the ITRs and arrangement of ORFs within the terminal regions. Each comparison gave the same conclusion: CMPV is the closest known virus to variola virus, the cause of smallpox.

Density increment and decreased survival of rat red blood cells induced by cadmium

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

Kunimoto, M.; Miura, T.

1986-01-01

Male Wistar rats were injected with CdCl/sub 2/ subcutaneously to examine in vivo effects of Cd on density and survival of red blood cells. During the 7 days after administration of 1.0 mg Cd/kg, the following sequence of events occurred: (1) a progressive increase in the amount of more dense red blood cells concomitant with a decrease in that of light red blood cells from the first to the third day; (2) an increase in the spleen weight at the third day; (3) a decrease in the hematocrit value and an increase in the amount of light red blood cellsmore » at the fifth day; and (4) a recovery of the hematocrit value at the seventh day. Five days after administration, the hematocrit value decreased in a dose-dependent mode and the decrease was significant at the 1% level at 1.0 and 1.5 mg Cd/kg. A highly significant splenomegaly was also observed at 0.5 to 1.5 mg Cd/kg. In order to label red blood cells in vivo, (/sup 3/H) diisopropylfluorophosphate ((/sup 3/H)DFP) was injected into rats. At Day 11, Cd at either 0.5 or 1.0 mg/kg was administered to (/sup 3/H)DFP-prelabeled animals. Cd administration accelerated /sup 3/H-labeled red cell clearance from the blood. Six days after Cd administration, the radioactivity of red blood cells was 76 and 68% of the control at 0.5 and 1.0 mg Cd/kg, respectively. In vitro treatment of rat red density and accelerated in vivo clearance of red blood cells from the recipient circulation. These results show that Cd at low dose can cause anemia by increasing red cell density and by accelerating red cell sequestration, presumably in the spleen.« less

Supermassive black holes and central star clusters: Connection with the host galaxy kinematics and color

NASA Astrophysics Data System (ADS)

Zasov, A. V.; Cherepashchuk, A. M.

2013-11-01

The relationship between the masses of the central, supermassive black holes ( M bh) and of the nuclear star clusters ( M nc) of disk galaxies with various parameters galaxies are considered: the rotational velocity at R = 2 kpc V (2), the maximum rotational velocity V max, the indicative dynamical mass M 25, the integrated mass of the stellar population M *, and the integrated color index B-V. The rotational velocities andmasses of the central objects were taken from the literature. Themass M nc correlatesmore closely with the kinematic parameters and the disk mass than M bh, including with the velocity V max, which is closely related to the virial mass of the dark halo. On average, lenticular galaxies are characterized by higher masses M bh compared to other types of galaxies with similar characteristics. The dependence of the blackhole mass on the color index is bimodal: galaxies of the red group (red-sequence) with B-V >0.6-0.7 which are mostly early-type galaxies with weak star formation, differ appreciably from blue galaxies, which have higher values of M nc and M bh. At the dependences we consider between the masses of the central objects and the parameters of the host galaxies (except for the dependence of M bh on the central velocity dispersion), the red-group galaxies have systematically higher M bh values, even when the host-galaxy parameters are similar. In contrast, in the case of nuclear star clusters, the blue and red galaxies form unified sequences. The results agree with scenarios in which most red-group galaxies form as a result of the partial or complete loss of interstellar gas in a stage of high nuclear activity in galaxies whose central black-hole masses exceed 106-107 M ⊙ (depending on the mass of the galaxy itself). The bulk of disk galaxies with M bh > 107 M ⊙ are lenticular galaxies (types S0, E/S0) whose disks are practically devoid of gas.

ASTEROSEISMOLOGY OF RED GIANTS FROM THE FIRST FOUR MONTHS OF KEPLER DATA: GLOBAL OSCILLATION PARAMETERS FOR 800 STARS

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

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

2010-11-10

We have studied solar-like oscillations in {approx}800 red giant stars using Kepler long-cadence photometry. The sample includes stars ranging in evolution from the lower part of the red giant branch to the helium main sequence. We investigate the relation between the large frequency separation ({Delta}{nu}) and the frequency of maximum power ({nu}{sub max}) and show that it is different for red giants than for main-sequence stars, which is consistent with evolutionary models and scaling relations. The distributions of {nu}{sub max} and {Delta}{nu} are in qualitative agreement with a simple stellar population model of the Kepler field, including the first evidencemore » for a secondary clump population characterized by M {approx}> 2 M{sub sun} and {nu}{sub max} {approx_equal} 40-110 {mu}Hz. We measured the small frequency separations {delta}{nu}{sub 02} and {delta}{nu}{sub 01} in over 400 stars and {delta}{nu}{sub 03} in over 40. We present C-D diagrams for l = 1, 2, and 3 and show that the frequency separation ratios {delta}{nu}{sub 02}/{Delta}{nu} and {delta}{nu}{sub 01}/{Delta}{nu} have opposite trends as a function of {Delta}{nu}. The data show a narrowing of the l = 1 ridge toward lower {nu}{sub max}, in agreement with models predicting more efficient mode trapping in stars with higher luminosity. We investigate the offset {epsilon} in the asymptotic relation and find a clear correlation with {Delta}{nu}, demonstrating that it is related to fundamental stellar parameters. Finally, we present the first amplitude-{nu}{sub max} relation for Kepler red giants. We observe a lack of low-amplitude stars for {nu}{sub max} {approx}> 110 {mu}Hz and find that, for a given {nu}{sub max} between 40 and 110 {mu}Hz, stars with lower {Delta}{nu} (and consequently higher mass) tend to show lower amplitudes than stars with higher {Delta}{nu}.« less

The origin of ultra-compact binaries

NASA Technical Reports Server (NTRS)

Hachisu, Izumi; Miyaji, Shigeki; Saio, Hideyuki

1987-01-01

The origin of ultra-compact binaries composed of a neutron star and a low-mass (about 0.06 solar mass) white dwarf is considered. Taking account of the systemic losses of mass and angular momentum, it was found that a serious difficulty exists in the scenarios which involve tidal captures of a normal star (a main sequence star or a red giant) by a neutron star. This difficulty can be avoided if a red giant star is captured by a massive white dwarf (M is approx. greater than 1.2 solar masses), which becomes a neutron star through the accretion induced collapse.

An experimental phylogeny to benchmark ancestral sequence reconstruction

PubMed Central

Randall, Ryan N.; Radford, Caelan E.; Roof, Kelsey A.; Natarajan, Divya K.; Gaucher, Eric A.

2016-01-01

Ancestral sequence reconstruction (ASR) is a still-burgeoning method that has revealed many key mechanisms of molecular evolution. One criticism of the approach is an inability to validate its algorithms within a biological context as opposed to a computer simulation. Here we build an experimental phylogeny using the gene of a single red fluorescent protein to address this criticism. The evolved phylogeny consists of 19 operational taxonomic units (leaves) and 17 ancestral bifurcations (nodes) that display a wide variety of fluorescent phenotypes. The 19 leaves then serve as ‘modern' sequences that we subject to ASR analyses using various algorithms and to benchmark against the known ancestral genotypes and ancestral phenotypes. We confirm computer simulations that show all algorithms infer ancient sequences with high accuracy, yet we also reveal wide variation in the phenotypes encoded by incorrectly inferred sequences. Specifically, Bayesian methods incorporating rate variation significantly outperform the maximum parsimony criterion in phenotypic accuracy. Subsampling of extant sequences had minor effect on the inference of ancestral sequences. PMID:27628687

Regulation of the Human Endogenous Retrovirus K (HML-2) Transcriptome by the HIV-1 Tat Protein

PubMed Central

Gonzalez-Hernandez, Marta J.; Cavalcoli, James D.; Sartor, Maureen A.; Contreras-Galindo, Rafael; Meng, Fan; Dai, Manhong; Dube, Derek; Saha, Anjan K.; Gitlin, Scott D.; Omenn, Gilbert S.; Kaplan, Mark H.

2014-01-01

ABSTRACT Approximately 8% of the human genome is made up of endogenous retroviral sequences. As the HIV-1 Tat protein activates the overall expression of the human endogenous retrovirus type K (HERV-K) (HML-2), we used next-generation sequencing to determine which of the 91 currently annotated HERV-K (HML-2) proviruses are regulated by Tat. Transcriptome sequencing of total RNA isolated from Tat- and vehicle-treated peripheral blood lymphocytes from a healthy donor showed that Tat significantly activates expression of 26 unique HERV-K (HML-2) proviruses, silences 12, and does not significantly alter the expression of the remaining proviruses. Quantitative reverse transcription-PCR validation of the sequencing data was performed on Tat-treated PBLs of seven donors using provirus-specific primers and corroborated the results with a substantial degree of quantitative similarity. IMPORTANCE The expression of HERV-K (HML-2) is tightly regulated but becomes markedly increased following infection with HIV-1, in part due to the HIV-1 Tat protein. The findings reported here demonstrate the complexity of the genome-wide regulation of HERV-K (HML-2) expression by Tat. This work also demonstrates that although HERV-K (HML-2) proviruses in the human genome are highly similar in terms of DNA sequence, modulation of the expression of specific proviruses in a given biological situation can be ascertained using next-generation sequencing and bioinformatics analysis. PMID:24872592

Isolation of anonymous DNA sequences from within a submicroscopic X chromosomal deletion in a patient with choroideremia, deafness, and mental retardation

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

Nussbaum, R.L.; Lesko, J.G.; Lewis, R.A.

1987-09-01

Choroideremia, an X-chromosome linked retinal dystrophy of unknown pathogenesis, causes progressive nightblindness and eventual central blindness in affected males by the third to fourth decade of life. Choroideremia has been mapped to Xq13-21 by tight linkage to restriction fragment length polymorphism loci. The authors have recently identified two families in which choroideremia is inherited with mental retardation and deafness. In family XL-62, an interstitial deletion Xq21 is visible by cytogenetic analysis and two linked anonymous DNA markers, DXYS1 and DXS72, are deleted. In the second family, XL-45, an interstitial deletion was suspected on phenotypic grounds but could not be confirmedmore » by high-resolution cytogenetic analysis. They used phenol-enhanced reassociation of 48,XXXX DNA in competition with excess XL-45 DNA to generate a library of cloned DNA enriched for sequences that might be deleted in XL-45. Two of the first 83 sequences characterized from the library were found to be deleted in probands from family XL-45 as well as from family XL-62. Isolation of these sequences proves that XL-45 does contain a submicroscopic deletion and provides a starting point for identifying overlapping genomic sequences that span the XL-45 deletion. Each overlapping sequence will be studied to identify exons from the choroideremia locus.« less

Whole-Genome Sequencing and Comparative Genome Analysis of Bacillus subtilis Strains Isolated from Non-Salted Fermented Soybean Foods.

PubMed

Kamada, Mayumi; Hase, Sumitaka; Fujii, Kazushi; Miyake, Masato; Sato, Kengo; Kimura, Keitarou; Sakakibara, Yasubumi

2015-01-01

Bacillus subtilis is the main component in the fermentation of soybeans. To investigate the genetics of the soybean-fermenting B. subtilis strains and its relationship with the productivity of extracellular poly-γ-glutamic acid (γPGA), we sequenced the whole genome of eight B. subtilis stains isolated from non-salted fermented soybean foods in Southeast Asia. Assembled nucleotide sequences were compared with those of a natto (fermented soybean food) starter strain B. subtilis BEST195 and the laboratory standard strain B. subtilis 168 that is incapable of γPGA production. Detected variants were investigated in terms of insertion sequences, biotin synthesis, production of subtilisin NAT, and regulatory genes for γPGA synthesis, which were related to fermentation process. Comparing genome sequences, we found that the strains that produce γPGA have a deletion in a protein that constitutes the flagellar basal body, and this deletion was not found in the non-producing strains. We further identified diversity in variants of the bio operon, which is responsible for the biotin auxotrophism of the natto starter strains. Phylogenetic analysis using multilocus sequencing typing revealed that the B. subtilis strains isolated from the non-salted fermented soybeans were not clustered together, while the natto-fermenting strains were tightly clustered; this analysis also suggested that the strain isolated from "Tua Nao" of Thailand traces a different evolutionary process from other strains.

Microsatellite Markers for Raspberries and Blackberries

USDA-ARS?s Scientific Manuscript database

Twelve microsatellites were isolated from SSR-enriched genomic libraries of Rubus idaeus L.‘Meeker’ red raspberry (diploid) and R. loganobaccus L. H. Bailey ‘Marion’ blackberry-raspberry hybrid (hexaploid). These primer pairs, with the addition of one developed from a GenBank R. idaeus sequence, w...

Lifestyles of the Stars.

ERIC Educational Resources Information Center

National Aeronautics and Space Administration, Cocoa Beach, FL. John F. Kennedy Space Center.

Some general information on stars is provided in this National Aeronautics and Space Administration pamphlet. Topic areas briefly discussed are: (1) the birth of a star; (2) main sequence stars; (3) red giants; (4) white dwarfs; (5) neutron stars; (6) supernovae; (7) pulsars; and (8) black holes. (JN)

Supernova 1987A - the evolution from blue to red

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

Tuchman, Y.; Wheeler, J.C.

1989-09-01

The evolution of stars with mass comparable to that of the progenitor of SN 1987A from the main sequence to the Hayashi track is critically examined to determine why some models evolve to the red on nuclear time scales, some on thermal time scales, and some not at all. Thermal equilibrium solutions to a parametrized series of structural models with active hydrogen burning shells have two stable solutions with different T(eff) for the same helium core M(He) mass and a minimum M(He) below which no blue thermal equlibrium solution is possible. The dependence of the equilibrium solutions on stellar mass,more » envelope composition, and mass loss are investigated. The solutions quantitatively account for the 'gap' in the HR diagrams of massive stars in the Galaxy and LMC and suggest that the outer envelopes are not substantially enriched in helium during the first passage from the main sequence to the Hayashi track. 23 refs.« less

Noninvasive Antenatal Determination of Fetal Blood Group Using Next-Generation Sequencing

PubMed Central

Rieneck, Klaus; Clausen, Frederik Banch; Dziegiel, Morten Hanefeld

2016-01-01

Hemolytic disease of the fetus and newborn (HDFN) is a condition characterized by a decreased lifespan of fetal red blood cells caused by maternally produced allospecific antibodies transferred to the fetus during pregnancy. The antibodies bind to the corresponding blood group antigens on fetal red blood cells and induce hemolysis. Cell-free DNA derived from the conceptus circulates in maternal blood. Using next-generation sequencing (NGS), it can be determined if this cell-free fetal DNA encodes the corresponding blood group antigen that is the target of the maternal allospecific antibodies. This determination carries no risk to the fetus. It is important to determine if the fetus is at risk of hemolysis to enable timely intervention. Many tests for blood groups are based solely on the presence or absence of a single nucleotide polymorphism (SNP). Antenatal determination of fetal blood group by NGS analysis holds advantages over polymerase chain reaction (PCR) determination based on allele specific amplification. PMID:26511760

HABITABLE ZONES OF POST-MAIN SEQUENCE STARS

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

Ramirez, Ramses M.; Kaltenegger, Lisa

Once a star leaves the main sequence and becomes a red giant, its Habitable Zone (HZ) moves outward, promoting detectable habitable conditions at larger orbital distances. We use a one-dimensional radiative-convective climate and stellar evolutionary models to calculate post-MS HZ distances for a grid of stars from 3700 to 10,000 K (∼M1 to A5 stellar types) for different stellar metallicities. The post-MS HZ limits are comparable to the distances of known directly imaged planets. We model the stellar as well as planetary atmospheric mass loss during the Red Giant Branch (RGB) and Asymptotic Giant Branch (AGB) phases for super-Moons tomore » super-Earths. A planet can stay between 200 million years up to 9 Gyr in the post-MS HZ for our hottest and coldest grid stars, respectively, assuming solar metallicity. These numbers increase for increased stellar metallicity. Total atmospheric erosion only occurs for planets in close-in orbits. The post-MS HZ orbital distances are within detection capabilities of direct imaging techniques.« less

On the non-variability of HR 7653 (15 Vul) based on BRITE data

NASA Astrophysics Data System (ADS)

Smalley, B.; Paunzen, E.; Lüftinger, T.; Moffat, A. F. J.; Pigulski, A.; Rucinski, S.; Sikora, J.; Wade, G. A.; Weiss, W.; BEST

2018-02-01

We present space-based BRITE photometric observations of the metallic line (CP1) star HR 7653 (15 Vul). This chemically peculiar star of the upper main sequence was suspected to show variability due to rotation and a magnetic field. Such a variability is quite unusual among the, in general, non-magnetic CP1 stars. We investigated the astrophysical parameters of HR 7653 placing it close to the terminal age main sequence or even in the subgiant phase. The longest BRITE data set has a time base of 18.01 d from which we conclude that there are no coherent long-period variations (>1 d) visible above 2.1 mmag in the red and 6.6 mmag in the blue. Furthermore, we searched for δ Scuti type pulsations. On the basis of a discrete Fourier analysis method, we find no peaks in the Fourier spectra above 0.5 mmag and 8.6 mmag, for the red and blue filters, respectively.

Mapping-by-Sequencing Identifies HvPHYTOCHROME C as a Candidate Gene for the early maturity 5 Locus Modulating the Circadian Clock and Photoperiodic Flowering in Barley

PubMed Central

Pankin, Artem; Campoli, Chiara; Dong, Xue; Kilian, Benjamin; Sharma, Rajiv; Himmelbach, Axel; Saini, Reena; Davis, Seth J; Stein, Nils; Schneeberger, Korbinian; von Korff, Maria

2014-01-01

Phytochromes play an important role in light signaling and photoperiodic control of flowering time in plants. Here we propose that the red/far-red light photoreceptor HvPHYTOCHROME C (HvPHYC), carrying a mutation in a conserved region of the GAF domain, is a candidate underlying the early maturity 5 locus in barley (Hordeum vulgare L.). We fine mapped the gene using a mapping-by-sequencing approach applied on the whole-exome capture data from bulked early flowering segregants derived from a backcross of the Bowman(eam5) introgression line. We demonstrate that eam5 disrupts circadian expression of clock genes. Moreover, it interacts with the major photoperiod response gene Ppd-H1 to accelerate flowering under noninductive short days. Our results suggest that HvPHYC participates in transmission of light signals to the circadian clock and thus modulates light-dependent processes such as photoperiodic regulation of flowering. PMID:24996910

Lung fluke (Paragonimus africanus) infects Nigerian red-capped mangabeys and causes respiratory disease

PubMed Central

Friant, Sagan; Brown, Kelsey; Saari, Mason T.; Segel, Nicholas H.; Slezak, Julia; Goldberg, Tony L.

2015-01-01

Eggs of the lung fluke genus Paragonimus were detected in red-capped mangabeys (Cercocebus torquatus) in Nigeria. We assess the role of these primates as potential sylvatic hosts and the clinical effects of the parasite on monkeys. DNA sequenced from eggs in feces were 100% identical in the ITS2 region to Paragonimus africanus sequences from humans in Cameroon. Paragonimus-positive monkeys coughed more than uninfected monkeys. Experimental de-worming led to reduction in parasite intensity and a corresponding reduction of coughing to baseline levels in infected monkeys. This report provides the first evidence of Paragonimus sp. in C. torquatus, of P. africanus in Nigerian wildlife, and the first molecular evidence of the parasite in African wildlife. Coughing, sometimes interpreted as a communication behavior in primates, can actually indicate infection with lung parasites. Observations of coughing in primates may, in turn, provide a useful mechanism for surveillance of Paragonimus spp, which are re-emerging human pathogens, in wildlife reservoirs. PMID:26543803

Lung fluke (Paragonimus africanus) infects Nigerian red-capped mangabeys and causes respiratory disease.

PubMed

Friant, Sagan; Brown, Kelsey; Saari, Mason T; Segel, Nicholas H; Slezak, Julia; Goldberg, Tony L

2015-12-01

Eggs of the lung fluke genus Paragonimus were detected in red-capped mangabeys (Cercocebus torquatus) in Nigeria. We assess the role of these primates as potential sylvatic hosts and the clinical effects of the parasite on monkeys. DNA sequenced from eggs in feces were 100% identical in the ITS2 region to Paragonimus africanus sequences from humans in Cameroon. Paragonimus-positive monkeys coughed more than uninfected monkeys. Experimental de-worming led to reduction in parasite intensity and a corresponding reduction of coughing to baseline levels in infected monkeys. This report provides the first evidence of Paragonimus sp. in C. torquatus, of P. africanus in Nigerian wildlife, and the first molecular evidence of the parasite in African wildlife. Coughing, sometimes interpreted as a communication behavior in primates, can actually indicate infection with lung parasites. Observations of coughing in primates may, in turn, provide a useful mechanism for surveillance of Paragonimus spp, which are re-emerging human pathogens, in wildlife reservoirs.

First molecular evidence of Hepatozoon canis infection in red foxes and golden jackals from Hungary

PubMed Central

2014-01-01

Background Recently, Hepatozoon canis infection has been detected among shepherd, hunting and stray dogs in the southern part of Hungary, which is considered to be free of Rhipicephalus sanguineus sensu lato and close to the border with Croatia. The aim of this study was to acquire information on the possibility that red foxes and/or golden jackals could play a role in the appearance and spread of H. canis in Hungary. Methods A conventional PCR was used to amplify a 666 bp long fragment of the Hepatozoon 18S rRNA gene from blood samples collected from 334 foxes shot in 231 locations in 16 counties and 15 golden jackals shot in 9 locations in two southwestern counties close to Croatia. A second PCR assay was performed in some of the samples positive by the first PCR to amplify a larger segment (approximately 1500 bp) of the 18S rRNA gene of Hepatozoon spp. for further phylogenetic analysis. Results Hepatozoon infection was detected in canids shot in 30 locations and 9 counties. Altogether 26 foxes (8.0%, 95% CI: 5-11%) and 9 jackals (60%, 95% CI: 33-81%) were PCR positive. Hepatozoon canis sequences were obtained from 12 foxes and 7 jackals. DNA sequences from 16 animals were 99-100% similar to H. canis from Croatian foxes or dogs while two of the sequences were 99% similar to an Italian fox. Half (13/26) of the infected red foxes and all golden jackals were shot in the two southwestern counties. Conclusions This is the first report on molecular evidence of H. canis in red foxes (Vulpes vulpes) and golden jackals (Canis aureus) from Hungary, which is considered free from the tick vector of H. canis, R. sanguineus. Although no R. sanguineus sensu lato had been found on infected or non-infected wild canids, the detection of authochnous canine hepatozoonosis in Hungary might imply that the range of R. sanguineus sensu lato has reached this country. PMID:24985073

Metallicity Variations in the Type II Globular Cluster NGC 6934

NASA Astrophysics Data System (ADS)

Marino, A. F.; Yong, D.; Milone, A. P.; Piotto, G.; Lundquist, M.; Bedin, L. R.; Chené, A.-N.; Da Costa, G.; Asplund, M.; Jerjen, H.

2018-06-01

The Hubble Space Telescope photometric survey of Galactic globular clusters (GCs) has revealed a peculiar “chromosome map” for NGC 6934. In addition to a typical sequence, similar to that observed in Type I GCs, NGC 6934 displays additional stars on the red side, analogous to the anomalous Type II GCs, as defined in our previous work. We present a chemical abundance analysis of four red giants in this GC. Two stars are located on the chromosome map sequence common to all GCs, and another two lie on the additional sequence. We find (i) star-to-star Fe variations, with the two anomalous stars being enriched by ∼0.2 dex. Because of our small-size sample, this difference is at the ∼2.5σ level. (ii) There is no evidence for variations in the slow neutron-capture abundances over Fe, at odds with what is often observed in anomalous Type II GCs, e.g., M 22 and ω Centauri (iii) no large variations in light elements C, O, and Na, compatible with locations of the targets on the lower part of the chromosome map where such variations are not expected. Since the analyzed stars are homogeneous in light elements, the only way to reproduce the photometric splits on the sub-giant (SGB) and the red giant (RGB) branches is to assume that red RGB/faint SGB stars are enhanced in [Fe/H] by ∼0.2. This fact corroborates the spectroscopic evidence of a metallicity variation in NGC 6934. The observed chemical pattern resembles only partially the other Type II GCs, suggesting that NGC 6934 might belong either to a third class of GCs, or be a link between normal Type I and anomalous Type II GCs. Based on observations with the NASA/ESA Hubble Space Telescope, obtained at the Space Telescope Science Institute, which is operated by AURA, Inc., under NASA contract NAS 5-26555. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile, and Gemini Telescope at Canada–France–Hawaii Telescope.

Subsurface to substrate: dual-scale micro/nanofluidic networks for investigating transport anomalies in tight porous media.

PubMed

Kelly, Shaina A; Torres-Verdín, Carlos; Balhoff, Matthew T

2016-08-07

Micro/nanofluidic experiments in synthetic representations of tight porous media, often referred to as "reservoir-on-a-chip" devices, are an emerging approach to researching anomalous fluid transport trends in energy-bearing and fluid-sequestering geologic porous media. We detail, for the first time, the construction of dual-scale micro/nanofluidic devices that are relatively large-scale, two-dimensional network representations of granular and fractured nanoporous media. The fabrication scheme used in the development of the networks on quartz substrates (master patterns) is facile and replicable: transmission electron microscopy (TEM) grids with lacey carbon support film were used as shadow masks in thermal evaporation/deposition and reactive ion etch (RIE) was used for hardmask pattern transfer. The reported nanoscale network geometries are heterogeneous and composed of hydraulically resistive paths (throats) meeting at junctures (pores) to mimic the low topological connectivity of nanoporous sedimentary rocks such as shale. The geometry also includes homogenous microscale grid patterns that border the nanoscale networks and represent microfracture pathways. Master patterns were successfully replicated with a sequence of polydimethylsiloxane (PDMS) and Norland Optical Adhesive (NOA) 63 polymers. The functionality of the fabricated quartz and polymer nanofluidic devices was validated with aqueous imbibition experiments and differential interference contrast microscopy. These dual-scale fluidic devices are promising predictive tools for hypothesis testing and calibration against bulk fluid measurements in tight geologic, biologic, and synthetic porous material of similar dual-scale pore structure. Applications to shale/mudrock transport studies in particular are focused on herein.

Identification of Amplified Fragment Length Polymorphism (AFLP) Markers Tightly Associated with Drought Stress Gene in Male Sterile and Fertile Salvia miltiorrhiza Bunge

PubMed Central

Zhang, Yuejin; Guo, Lijun; Shu, Zhiming; Sun, Yiyue; Chen, Yuanyuan; Liang, Zongsuo; Guo, Hongbo

2013-01-01

Consistent grain yield in drought environment has attracted wide attention due to global climate change. However, the important drought-related traits/genes in crops have been rarely reported. Many near-isogenic lines (NILs) of male sterile and fertile Salvia miltiorrhiza have been obtained in our previous work through testcross and backcross in continuous field experiments conducted in 2006–2009. Both segregating sterile and fertile populations were subjected to bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) with 384 and 170 primer combinations, respectively. One out of 14 AFLP markers (E9/M3246) was identified in treated fertile population as tightly linked to the drought stress gene with a recombination frequency of 6.98% and at a distance of 7.02 cM. One of 15 other markers (E2/M5357) was identified in a treated sterile population that is closely associated with the drought stress gene. It had a recombination frequency of 4.65% and at a distance of 4.66 cM. Interestingly, the E9/M3246 fragment was found to be identical to another AFLP fragment E11/M4208 that was tightly linked to the male sterile gene of S. miltiorrhiza with 95% identity and e-value 4 × 10−93. Blastn analysis suggested that the drought stress gene sequence showed higher identity with nucleotides in Arabidopsis chromosome 1–5. PMID:23525049

gyrB as a phylogenetic discriminator for members of the Bacillus anthracis-cereus-thuringiensis group

NASA Technical Reports Server (NTRS)

La Duc, Myron T.; Satomi, Masataka; Agata, Norio; Venkateswaran, Kasthuri

2004-01-01

Bacillus anthracis, the causative agent of the human disease anthrax, Bacillus cereus, a food-borne pathogen capable of causing human illness, and Bacillus thuringiensis, a well-characterized insecticidal toxin producer, all cluster together within a very tight clade (B. cereus group) phylogenetically and are indistinguishable from one another via 16S rDNA sequence analysis. As new pathogens are continually emerging, it is imperative to devise a system capable of rapidly and accurately differentiating closely related, yet phenotypically distinct species. Although the gyrB gene has proven useful in discriminating closely related species, its sequence analysis has not yet been validated by DNA:DNA hybridization, the taxonomically accepted "gold standard". We phylogenetically characterized the gyrB sequences of various species and serotypes encompassed in the "B. cereus group," including lab strains and environmental isolates. Results were compared to those obtained from analyses of phenotypic characteristics, 16S rDNA sequence, DNA:DNA hybridization, and virulence factors. The gyrB gene proved more highly differential than 16S, while, at the same time, as analytical as costly and laborious DNA:DNA hybridization techniques in differentiating species within the B. cereus group.

Detection of porcine circovirus type 2 in pigs imported from Indonesia.

PubMed

Manokaran, Gayathri; Lin, Yueh-Nuo; Soh, Moi-Lien; Lim, Elizabeth Ai-Sim; Lim, Chee-Wee; Tan, Boon-Huan

2008-11-25

We have detected the presence of porcine circovirus (PCV) type 2 in Indonesian pigs imported to Singapore for food consumption. A total of three viral isolates were identified, and to genetically characterise them further, their full genomes were sequenced. Each genome showed a typical organization of PCV type 2, with the three isolates sharing similar genome lengths of 1767 nucleotide (nt) at high nt identities of 99.8-100%, further indicating that the viral isolates were quite homogeneous. Sequence analysis further revealed that the ORF2 genes contain the nt sequence CCCCGC (from nt position 262 to 267) that was previously reported to be associated with PCV type 2, group 1C. The phylogenetic tree was constructed for the ORF2 genes, and the PCV type 2 isolates distributed into two distinctive groups. The Indonesian PCV type 2 clustered tightly with one China isolate, accession number AY035820, as a sub-cluster in group 1C. The sequence and phylogenetic analyses both confirmed that the three Indonesian PCV type 2 isolates belong to group 1C, and that the genetic changes for the three Indonesian isolates were very stable, possibly due to the low-scale evolution.

Brain activation during anticipation of sound sequences.

PubMed

Leaver, Amber M; Van Lare, Jennifer; Zielinski, Brandon; Halpern, Andrea R; Rauschecker, Josef P

2009-02-25

Music consists of sound sequences that require integration over time. As we become familiar with music, associations between notes, melodies, and entire symphonic movements become stronger and more complex. These associations can become so tight that, for example, hearing the end of one album track can elicit a robust image of the upcoming track while anticipating it in total silence. Here, we study this predictive "anticipatory imagery" at various stages throughout learning and investigate activity changes in corresponding neural structures using functional magnetic resonance imaging. Anticipatory imagery (in silence) for highly familiar naturalistic music was accompanied by pronounced activity in rostral prefrontal cortex (PFC) and premotor areas. Examining changes in the neural bases of anticipatory imagery during two stages of learning conditional associations between simple melodies, however, demonstrates the importance of fronto-striatal connections, consistent with a role of the basal ganglia in "training" frontal cortex (Pasupathy and Miller, 2005). Another striking change in neural resources during learning was a shift between caudal PFC earlier to rostral PFC later in learning. Our findings regarding musical anticipation and sound sequence learning are highly compatible with studies of motor sequence learning, suggesting common predictive mechanisms in both domains.

Brain Activation During Anticipation of Sound Sequences

PubMed Central

Leaver, Amber M.; Van Lare, Jennifer; Zielinski, Brandon; Halpern, Andrea R.; Rauschecker, Josef P.

2010-01-01

Music consists of sound sequences that require integration over time. As we become familiar with music, associations between notes, melodies, and entire symphonic movements become stronger and more complex. These associations can become so tight that, for example, hearing the end of one album track can elicit a robust image of the upcoming track while anticipating it in total silence. Here we study this predictive “anticipatory imagery” at various stages throughout learning and investigate activity changes in corresponding neural structures using functional magnetic resonance imaging (fMRI). Anticipatory imagery (in silence) for highly familiar naturalistic music was accompanied by pronounced activity in rostral prefrontal cortex (PFC) and premotor areas. Examining changes in the neural bases of anticipatory imagery during two stages of learning conditional associations between simple melodies, however, demonstrates the importance of fronto-striatal connections, consistent with a role of the basal ganglia in “training” frontal cortex (Pasupathy and Miller, 2005). Another striking change in neural resources during learning was a shift between caudal PFC earlier to rostral PFC later in learning. Our findings regarding musical anticipation and sound sequence learning are highly compatible with studies of motor sequence learning, suggesting common predictive mechanisms in both domains. PMID:19244522

Electron microscopic analysis and structural characterization of novel NADP(H)-containing methanol: N,N'-dimethyl-4-nitrosoaniline oxidoreductases from the gram-positive methylotrophic bacteria Amycolatopsis methanolica and Mycobacterium gastri MB19.

PubMed Central

Bystrykh, L V; Vonck, J; van Bruggen, E F; van Beeumen, J; Samyn, B; Govorukhina, N I; Arfman, N; Duine, J A; Dijkhuizen, L

1993-01-01

The quaternary protein structure of two methanol:N,N'-dimethyl-4-nitrosoaniline (NDMA) oxidoreductases purified from Amycolatopsis methanolica and Mycobacterium gastri MB19 was analyzed by electron microscopy and image processing. The enzymes are decameric proteins (displaying fivefold symmetry) with estimated molecular masses of 490 to 500 kDa based on their subunit molecular masses of 49 to 50 kDa. Both methanol:NDMA oxidoreductases possess a tightly but noncovalently bound NADP(H) cofactor at an NADPH-to-subunit molar ratio of 0.7. These cofactors are redox active toward alcohol and aldehyde substrates. Both enzymes contain significant amounts of Zn2+ and Mg2+ ions. The primary amino acid sequences of the A. methanolica and M. gastri MB19 methanol:NDMA oxidoreductases share a high degree of identity, as indicated by N-terminal sequence analysis (63% identity among the first 27 N-terminal amino acids), internal peptide sequence analysis, and overall amino acid composition. The amino acid sequence analysis also revealed significant similarity to a decameric methanol dehydrogenase of Bacillus methanolicus C1. Images PMID:8449887

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

PubMed Central

Koonin, Eugene V.; Wolf, Yuri I.

2008-01-01

The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution. PMID:18948295

TAS2R38 bitter taste genetics, dietary vitamin C, and both natural and synthetic dietary folic acid predict folate status, a key micronutrient in the pathoaetiology of adenomatous polyps.

PubMed

Lucock, Mark; Ng, Xiaowei; Boyd, Lyndell; Skinner, Virginia; Wai, Ron; Tang, Sa; Naylor, Charlotte; Yates, Zoë; Choi, Jeong-Hwa; Roach, Paul; Veysey, Martin

2011-08-01

Taste perception may influence dietary preferences and nutrient intakes contributing to diet-related disease susceptibility. This study examined bitter taste genetics and whether variation in the TAS2R38 gene at three polymorphic loci (A49P, V262A and I296V) could alter dietary and systemic folate levels and dietary vitamin C intake, and whether a nutrigenetic circuit existed that might link bitter taste, folate/antioxidant status and risk for a colonic adenomatous polyp. TAS2R38 diplotype predicted bitter taste (PROP) phenotype (p value <0.00001) and red cell folate status (p=0.0179) consistent with the diplotype that has the broadest range of bitter perception (AVI/PAV) also possessing the highest average red cell folate value. However, TAS2R38 diplotype did not predict dietary intake of methylfolic acid, pteroylmonoglutamic acid or total folic acid. Neither did it predict dietary intake of vitamin C. Despite this, intake of dietary folate predicts red cell folate with analysis pointing to a key nutrient-nutrient interaction between vitamin C intake and systemic folate status. Analysis of 38 patients with an adenomatous polyp and 164 controls showed that individually, dietary nutrient intake, nutrient status and taste diplotype did not influence polyp risk. However, red cell folate status (in individuals below the population median value) did interact with bitter taste diplotype (AVI/PAV) to predict polyp risk (p=0.0145). Furthermore, synthetic folic acid (below median intake) was statistically associated with adenoma occurrence (p=0.0215); individuals with adenomatous polyps had a 1.77× higher intake than controls. Additionally, stepwise regression taking account of all dietary nutrients showed a tight relationship between methylfolic acid (but not pteroylmonoglutamic acid) intake and red cell folate level in those with a low folate status and occurrence of an adenomatous polyp (p=0.0039). These findings point to a role for folate in the pathoaetiology of adenomatous polyps, with the natural and synthetic vitamers not necessarily having the same biological effect. This journal is © The Royal Society of Chemistry 2011

Construction and Evaluation of Normalized cDNA Libraries Enriched with Full-Length Sequences for Rapid Discovery of New Genes from Sisal (Agave sisalana Perr.) Different Developmental Stages

PubMed Central

Zhou, Wen-Zhao; Zhang, Yan-Mei; Lu, Jun-Ying; Li, Jun-Feng

2012-01-01

To provide a resource of sisal-specific expressed sequence data and facilitate this powerful approach in new gene research, the preparation of normalized cDNA libraries enriched with full-length sequences is necessary. Four libraries were produced with RNA pooled from Agave sisalana multiple tissues to increase efficiency of normalization and maximize the number of independent genes by SMART™ method and the duplex-specific nuclease (DSN). This procedure kept the proportion of full-length cDNAs in the subtracted/normalized libraries and dramatically enhanced the discovery of new genes. Sequencing of 3875 cDNA clones of libraries revealed 3320 unigenes with an average insert length about 1.2 kb, indicating that the non-redundancy of libraries was about 85.7%. These unigene functions were predicted by comparing their sequences to functional domain databases and extensively annotated with Gene Ontology (GO) terms. Comparative analysis of sisal unigenes and other plant genomes revealed that four putative MADS-box genes and knotted-like homeobox (knox) gene were obtained from a total of 1162 full-length transcripts. Furthermore, real-time PCR showed that the characteristics of their transcripts mainly depended on the tight expression regulation of a number of genes during the leaf and flower development. Analysis of individual library sequence data indicated that the pooled-tissue approach was highly effective in discovering new genes and preparing libraries for efficient deep sequencing. PMID:23202944

Molecular Detection of Avian Pathogens in Poultry Red Mite (Dermanyssus gallinae) Collected in Chicken Farms

PubMed Central

HUONG, Chu Thi Thanh; MURANO, Takako; UNO, Yukiko; USUI, Tatsufumi; YAMAGUCHI, Tsuyoshi

2014-01-01

Poultry red mite (PRM, Dermanyssus gallinae) is a blood-sucking ectoparasite as well as a possible vector of several avian pathogens. In this study, to define the role of PRM in the prevalence of avian infectious agents, we used polymerase chain reaction (PCR) to check for the presence of seven pathogens: Avipox virus (APV), Fowl Adenovirus (FAdV), Marek’s disease virus (MDV), Erysipelothrix rhusiopathiae (ER), Salmonella enterica (SE), Mycoplasma synoviae (MS) and Mycoplasma gallisepticum (MG). A total of 159 PRM samples collected between 2004 and 2012 from 142 chicken farms in 38 prefectures in Japan were examined. APV DNA was detected in 22 samples (13.8%), 19 of which were wild-type APV. 16S ribosomal RNA (16S rRNA) of MS was detected in 15 samples (9.4%), and the mgc2 gene of MG was detected in 2 samples (1.3%). Eight of 15 MS 16S rRNA sequences differed from the vaccine sequence, indicating they were wild-type strains, while both of the MG mgc2 gene sequences detected were identical to the vaccine sequences. Of these avian pathogen-positive mite samples, three were positive for both wild-types of APV and MS. On the other hand, the DNAs of ER, SE, FAdV and MDV were not detected in any samples. These findings indicated that PRM can harbor the wild-type pathogens and might play a role as a vector in spreading these diseases in farms. PMID:25649939

Molecular detection of avian pathogens in poultry red mite (Dermanyssus gallinae) collected in chicken farms.

PubMed

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

2014-12-01

Poultry red mite (PRM, Dermanyssus gallinae) is a blood-sucking ectoparasite as well as a possible vector of several avian pathogens. In this study, to define the role of PRM in the prevalence of avian infectious agents, we used polymerase chain reaction (PCR) to check for the presence of seven pathogens: Avipox virus (APV), Fowl Adenovirus (FAdV), Marek's disease virus (MDV), Erysipelothrix rhusiopathiae (ER), Salmonella enterica (SE), Mycoplasma synoviae (MS) and Mycoplasma gallisepticum (MG). A total of 159 PRM samples collected between 2004 and 2012 from 142 chicken farms in 38 prefectures in Japan were examined. APV DNA was detected in 22 samples (13.8%), 19 of which were wild-type APV. 16S ribosomal RNA (16S rRNA) of MS was detected in 15 samples (9.4%), and the mgc2 gene of MG was detected in 2 samples (1.3%). Eight of 15 MS 16S rRNA sequences differed from the vaccine sequence, indicating they were wild-type strains, while both of the MG mgc2 gene sequences detected were identical to the vaccine sequences. Of these avian pathogen-positive mite samples, three were positive for both wild-types of APV and MS. On the other hand, the DNAs of ER, SE, FAdV and MDV were not detected in any samples. These findings indicated that PRM can harbor the wild-type pathogens and might play a role as a vector in spreading these diseases in farms.

Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple

PubMed Central

Chagné, David; Carlisle, Charmaine M; Blond, Céline; Volz, Richard K; Whitworth, Claire J; Oraguzie, Nnadozie C; Crowhurst, Ross N; Allan, Andrew C; Espley, Richard V; Hellens, Roger P; Gardiner, Susan E

2007-01-01

Background Integrating plant genomics and classical breeding is a challenge for both plant breeders and molecular biologists. Marker-assisted selection (MAS) is a tool that can be used to accelerate the development of novel apple varieties such as cultivars that have fruit with anthocyanin through to the core. In addition, determining the inheritance of novel alleles, such as the one responsible for red flesh, adds to our understanding of allelic variation. Our goal was to map candidate anthocyanin biosynthetic and regulatory genes in a population segregating for the red flesh phenotypes. Results We have identified the Rni locus, a major genetic determinant of the red foliage and red colour in the core of apple fruit. In a population segregating for the red flesh and foliage phenotype we have determined the inheritance of the Rni locus and DNA polymorphisms of candidate anthocyanin biosynthetic and regulatory genes. Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) in the candidate genes were also located on an apple genetic map. We have shown that the MdMYB10 gene co-segregates with the Rni locus and is on Linkage Group (LG) 09 of the apple genome. Conclusion We have performed candidate gene mapping in a fruit tree crop and have provided genetic evidence that red colouration in the fruit core as well as red foliage are both controlled by a single locus named Rni. We have shown that the transcription factor MdMYB10 may be the gene underlying Rni as there were no recombinants between the marker for this gene and the red phenotype in a population of 516 individuals. Associating markers derived from candidate genes with a desirable phenotypic trait has demonstrated the application of genomic tools in a breeding programme of a horticultural crop species. PMID:17608951