Halo Nuclei

NASA Astrophysics Data System (ADS)

Al-Khalili, Jim

2017-10-01

While neutron halos were discovered 30 years ago, this is the first book written on the subject of this exotic form of nuclei that typically contain many more neutrons than stable isotopes of those elements. It provides an introductory description of the halo and outlines the discovery and evidence for its existence. It also discusses different theoretical models of the halo's structure as well as models and techniques in reaction theory that have allowed us to study the halo. This is written at the graduate student (starting at PhD) level. The author of the book, Jim Al-Khalili, is a theoretician who published some of the key papers on the structure of the halo in the mid and late 90s and was the first to determine its true size. This monograph is based on review articles he has written on the mathematical models used to determine the halo structure and the reactions used to model that structure.

Subhalo demographics in the Illustris simulation: effects of baryons and halo-to-halo variation

NASA Astrophysics Data System (ADS)

Chua, Kun Ting Eddie; Pillepich, Annalisa; Rodriguez-Gomez, Vicente; Vogelsberger, Mark; Bird, Simeon; Hernquist, Lars

2017-12-01

We study the abundance of subhaloes in the hydrodynamical cosmological simulation Illustris, which includes both baryons and dark matter in a cold dark matter volume 106.5 Mpc a side. We compare Illustris to its dark-matter only (DMO) analogue, Illustris-Dark and quantify the effects of baryonic processes on the demographics of subhaloes in the host mass range 1011-3 × 1014 M⊙. We focus on both the evolved (z = 0) subhalo cumulative mass functions (SHMF) and the statistics of subhaloes ever accreted, i.e. infall SHMF. We quantify the variance in subhalo abundance at fixed host mass and investigate the physical reasons responsible for such scatter. We find that in Illustris, baryonic physics impacts both the infall and z = 0 subhalo abundance by tilting the DMO function and suppressing the abundance of low-mass subhaloes. The breaking of self-similarity in the subhalo abundance at z = 0 is enhanced by the inclusion of baryonic physics. The non-monotonic alteration of the evolved subhalo abundances can be explained by the modification of the concentration-mass relation of Illustris hosts compared to Illustris-Dark. Interestingly, the baryonic implementation in Illustris does not lead to an increase in the halo-to-halo variation compared to Illustris-Dark. In both cases, the normalized intrinsic scatter today is larger for Milky Way-like haloes than for cluster-sized objects. For Milky Way-like haloes, it increases from about eight per cent at infall to about 25 per cent at the current epoch. In both runs, haloes of fixed mass formed later host more subhaloes than early formers.

Cloud computing for comparative genomics.

PubMed

Wall, Dennis P; Kudtarkar, Parul; Fusaro, Vincent A; Pivovarov, Rimma; Patil, Prasad; Tonellato, Peter J

2010-05-18

Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD), to run within Amazon's Elastic Computing Cloud (EC2). We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems.

Cloud computing for comparative genomics

PubMed Central

2010-01-01

Background Large comparative genomics studies and tools are becoming increasingly more compute-expensive as the number of available genome sequences continues to rise. The capacity and cost of local computing infrastructures are likely to become prohibitive with the increase, especially as the breadth of questions continues to rise. Alternative computing architectures, in particular cloud computing environments, may help alleviate this increasing pressure and enable fast, large-scale, and cost-effective comparative genomics strategies going forward. To test this, we redesigned a typical comparative genomics algorithm, the reciprocal smallest distance algorithm (RSD), to run within Amazon's Elastic Computing Cloud (EC2). We then employed the RSD-cloud for ortholog calculations across a wide selection of fully sequenced genomes. Results We ran more than 300,000 RSD-cloud processes within the EC2. These jobs were farmed simultaneously to 100 high capacity compute nodes using the Amazon Web Service Elastic Map Reduce and included a wide mix of large and small genomes. The total computation time took just under 70 hours and cost a total of $6,302 USD. Conclusions The effort to transform existing comparative genomics algorithms from local compute infrastructures is not trivial. However, the speed and flexibility of cloud computing environments provides a substantial boost with manageable cost. The procedure designed to transform the RSD algorithm into a cloud-ready application is readily adaptable to similar comparative genomics problems. PMID:20482786

How do stars affect ψDM halos?

NASA Astrophysics Data System (ADS)

Chan, James H. H.; Schive, Hsi-Yu; Woo, Tak-Pong; Chiueh, Tzihong

2018-04-01

Wave dark matter (ψDM) predicts a compact soliton core and a granular halo in every galaxy. This work presents the first simulation study of an elliptical galaxy by including both stars and ψDM, focusing on the systematic changes of the central soliton and halo granules. With the addition of stars in the inner halo, we find the soliton core consistently becomes more prominent by absorbing mass from the host halo than that without stars, and the halo granules become "non-isothermal", "hotter" in the inner halo and "cooler" in the outer halo, as opposed to the isothermal halo in pure ψDM cosmological simulations. Moreover, the composite (star+ψDM) mass density is found to follow a r-2 isothermal profile near the half-light radius in most cases. Most striking is the velocity dispersion of halo stars that increases rapidly toward the galactic center by a factor of at least 2 inside the half-light radius caused by the deepened soliton gravitational potential, a result that compares favorably with observations of elliptical galaxies and bulges in spiral galaxies. However in some rare situations we find a phase segregation turning a compact distribution of stars into two distinct populations with high and very low velocity dispersions; while the high-velocity component mostly resides in the halo, the very low-velocity component is bound to the interior of the soliton core, resembling stars in faint dwarf spheroidal galaxies.

Halo assembly bias and the tidal anisotropy of the local halo environment

NASA Astrophysics Data System (ADS)

Paranjape, Aseem; Hahn, Oliver; Sheth, Ravi K.

2018-05-01

We study the role of the local tidal environment in determining the assembly bias of dark matter haloes. Previous results suggest that the anisotropy of a halo's environment (i.e. whether it lies in a filament or in a more isotropic region) can play a significant role in determining the eventual mass and age of the halo. We statistically isolate this effect, using correlations between the large-scale and small-scale environments of simulated haloes at z = 0 with masses between 1011.6 ≲ (m/h-1 M⊙) ≲ 1014.9. We probe the large-scale environment, using a novel halo-by-halo estimator of linear bias. For the small-scale environment, we identify a variable αR that captures the tidal anisotropy in a region of radius R = 4R200b around the halo and correlates strongly with halo bias at fixed mass. Segregating haloes by αR reveals two distinct populations. Haloes in highly isotropic local environments (αR ≲ 0.2) behave as expected from the simplest, spherically averaged analytical models of structure formation, showing a negative correlation between their concentration and large-scale bias at all masses. In contrast, haloes in anisotropic, filament-like environments (αR ≳ 0.5) tend to show a positive correlation between bias and concentration at any mass. Our multiscale analysis cleanly demonstrates how the overall assembly bias trend across halo mass emerges as an average over these different halo populations, and provides valuable insights towards building analytical models that correctly incorporate assembly bias. We also discuss potential implications for the nature and detectability of galaxy assembly bias.

Ebolavirus comparative genomics

DOE PAGES

Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; ...

2015-07-14

The 2014 Ebola outbreak in West Africa is the largest documented for this virus. We examine the dynamics of this genome, comparing more than one hundred currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus, and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of themore » same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP), and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. In conclusion, this information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies.« less

Halo vest effect on balance.

PubMed

Richardson, J K; Ross, A D; Riley, B; Rhodes, R L

2000-03-01

To determine the effect of a halo vest, a cervical orthosis, on clinically relevant balance parameters. Subjects performed unipedal stance (with eyes open and closed, on both firm and soft surfaces) and functional reach, with and without the application of a halo vest. A convenience sample of 12 healthy young subjects, with an equal number of men and women. Seconds for unipedal stance (maximum 45); inches for functional reach. Both unipedal stance times and functional reach (mean +/- standard deviation) were significantly decreased with the halo vest as compared to without it (29.1+/-5.8 vs. 32.8+/-6.4 seconds, p = .002; 12.9+/-1.4 vs. 15.1+/-2.1 inches, p<.01). A halo vest causes an acute impairment in balance in the healthy young. It is likely that the impairment would be greater in older or injured patients, thus increasing their risk for a fall, which could have devastating consequences.

Comparative Genomics in Homo sapiens.

PubMed

Oti, Martin; Sammeth, Michael

2018-01-01

Genomes can be compared at different levels of divergence, either between species or within species. Within species genomes can be compared between different subpopulations, such as human subpopulations from different continents. Investigating the genomic differences between different human subpopulations is important when studying complex diseases that are affected by many genetic variants, as the variants involved can differ between populations. The 1000 Genomes Project collected genome-scale variation data for 2504 human individuals from 26 different populations, enabling a systematic comparison of variation between human subpopulations. In this chapter, we present step-by-step a basic protocol for the identification of population-specific variants employing the 1000 Genomes data. These variants are subsequently further investigated for those that affect the proteome or RNA splice sites, to investigate potentially biologically relevant differences between the populations.

Historical halo displays as past weather indicator

NASA Astrophysics Data System (ADS)

Neuhäuser, Dagmar; Neuhäuser, Ralph

2017-04-01

Certain halo displays like the 22° circle were known to indicate specific weather pattern since millennia - as specified in Babylonian omina, Aristotle's Meteorology, farmers' weather lore, etc. Today, it is known that halo phenomena are due to refraction and reflection of sun and moon light in ice crystals in cirrus and cirrostratus, so that halo observations do indicate atmospheric conditions like temperature, humidity, pressure etc. in a few km height. The Astronomical Diaries of Babylonia have recorded both halo phenomena (circles, parhelia, etc.) and weather conditions (rain, clouds, etc.), so that we can use them to show statistically, whether, which and how fast halo phenomena are related to weather - for the last few centuries BC for Babylonia. We can then also compare the observations of Babylonian priests in the given BC epoch (without air and light pollution) with the last few decades of the modern epoch (with air and light pollution), where amateur halo observers have systematically recorded such phenomena (in Europe). Weather and climate are known to be partly driven by solar activity. Hence, one could also consider whether there is an indirect relation between halo displays as weather proxy and aurorae as solar activity proxy - if low solar activity leads to low pressure systems, one could expect more halos, preliminary studies show such a hint. For the last few decades, we have many halo observations, satellite imaging of the aurora oval, and many data on solar activity. A statistically sufficient amount of aurora and halo observations should be available for the historic time to investigate such a possible connection: halos were recorded very often in antiquity and the medieval times (as found in chronicles etc.), and modern scholarly catalogs of aurorae also often contain unrecognized halo displays.

Whole-genome sequencing for comparative genomics and de novo genome assembly.

PubMed

Benjak, Andrej; Sala, Claudia; Hartkoorn, Ruben C

2015-01-01

Next-generation sequencing technologies for whole-genome sequencing of mycobacteria are rapidly becoming an attractive alternative to more traditional sequencing methods. In particular this technology is proving useful for genome-wide identification of mutations in mycobacteria (comparative genomics) as well as for de novo assembly of whole genomes. Next-generation sequencing however generates a vast quantity of data that can only be transformed into a usable and comprehensible form using bioinformatics. Here we describe the methodology one would use to prepare libraries for whole-genome sequencing, and the basic bioinformatics to identify mutations in a genome following Illumina HiSeq or MiSeq sequencing, as well as de novo genome assembly following sequencing using Pacific Biosciences (PacBio).

Phytozome Comparative Plant Genomics Portal

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

Goodstein, David; Batra, Sajeev; Carlson, Joseph

2014-09-09

The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

The halo Boltzmann equation

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

Biagetti, Matteo; Desjacques, Vincent; Kehagias, Alex

2016-04-01

Dark matter halos are the building blocks of the universe as they host galaxies and clusters. The knowledge of the clustering properties of halos is therefore essential for the understanding of the galaxy statistical properties. We derive an effective halo Boltzmann equation which can be used to describe the halo clustering statistics. In particular, we show how the halo Boltzmann equation encodes a statistically biased gravitational force which generates a bias in the peculiar velocities of virialized halos with respect to the underlying dark matter, as recently observed in N-body simulations.

Orthology for comparative genomics in the mouse genome database.

PubMed

Dolan, Mary E; Baldarelli, Richard M; Bello, Susan M; Ni, Li; McAndrews, Monica S; Bult, Carol J; Kadin, James A; Richardson, Joel E; Ringwald, Martin; Eppig, Janan T; Blake, Judith A

2015-08-01

The mouse genome database (MGD) is the model organism database component of the mouse genome informatics system at The Jackson Laboratory. MGD is the international data resource for the laboratory mouse and facilitates the use of mice in the study of human health and disease. Since its beginnings, MGD has included comparative genomics data with a particular focus on human-mouse orthology, an essential component of the use of mouse as a model organism. Over the past 25 years, novel algorithms and addition of orthologs from other model organisms have enriched comparative genomics in MGD data, extending the use of orthology data to support the laboratory mouse as a model of human biology. Here, we describe current comparative data in MGD and review the history and refinement of orthology representation in this resource.

The halo model in a massive neutrino cosmology

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

Massara, Elena; Villaescusa-Navarro, Francisco; Viel, Matteo, E-mail: emassara@sissa.it, E-mail: villaescusa@oats.inaf.it, E-mail: viel@oats.inaf.it

2014-12-01

We provide a quantitative analysis of the halo model in the context of massive neutrino cosmologies. We discuss all the ingredients necessary to model the non-linear matter and cold dark matter power spectra and compare with the results of N-body simulations that incorporate massive neutrinos. Our neutrino halo model is able to capture the non-linear behavior of matter clustering with a ∼20% accuracy up to very non-linear scales of k = 10 h/Mpc (which would be affected by baryon physics). The largest discrepancies arise in the range k = 0.5 – 1 h/Mpc where the 1-halo and 2-halo terms are comparable and are present also inmore » a massless neutrino cosmology. However, at scales k < 0.2 h/Mpc our neutrino halo model agrees with the results of N-body simulations at the level of 8% for total neutrino masses of < 0.3 eV. We also model the neutrino non-linear density field as a sum of a linear and clustered component and predict the neutrino power spectrum and the cold dark matter-neutrino cross-power spectrum up to k = 1 h/Mpc with ∼30% accuracy. For masses below 0.15 eV the neutrino halo model captures the neutrino induced suppression, casted in terms of matter power ratios between massive and massless scenarios, with a 2% agreement with the results of N-body/neutrino simulations. Finally, we provide a simple application of the halo model: the computation of the clustering of galaxies, in massless and massive neutrinos cosmologies, using a simple Halo Occupation Distribution scheme and our halo model extension.« less

HaloSat - A CubeSat to Study the Hot Galactic Halo

NASA Astrophysics Data System (ADS)

Kaaret, Philip

2017-01-01

Observations of the nearby universe fail to locate about half of the baryons observed in the early universe. The missing baryons may be in hot galactic halos. HaloSat is a CubeSat designed to map oxygen line emission (O VII and O VIII) around the Milky Way in order to constrain the mass and spatial distribution of hot gas in the halo. HaloSat has a grasp competitive with current X-ray observatories. Its observing program will be optimized to minimize contributions from solar wind charge exchange (SWCX) emission that limit the accuracy of current measurements. We will describe the HaloSat mission concept, progress towards its implementation, and plans for archiving and distribution of the data.

Haemonchus contortus: Genome Structure, Organization and Comparative Genomics.

PubMed

Laing, R; Martinelli, A; Tracey, A; Holroyd, N; Gilleard, J S; Cotton, J A

2016-01-01

One of the first genome sequencing projects for a parasitic nematode was that for Haemonchus contortus. The open access data from the Wellcome Trust Sanger Institute provided a valuable early resource for the research community, particularly for the identification of specific genes and genetic markers. Later, a second sequencing project was initiated by the University of Melbourne, and the two draft genome sequences for H. contortus were published back-to-back in 2013. There is a pressing need for long-range genomic information for genetic mapping, population genetics and functional genomic studies, so we are continuing to improve the Wellcome Trust Sanger Institute assembly to provide a finished reference genome for H. contortus. This review describes this process, compares the H. contortus genome assemblies with draft genomes from other members of the strongylid group and discusses future directions for parasite genomics using the H. contortus model. Copyright © 2016 Elsevier Ltd. All rights reserved.

GenColors-based comparative genome databases for small eukaryotic genomes.

PubMed

Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

2013-01-01

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

Comparative Reannotation of 21 Aspergillus Genomes

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

Salamov, Asaf; Riley, Robert; Kuo, Alan

2013-03-08

We used comparative gene modeling to reannotate 21 Aspergillus genomes. Initial automatic annotation of individual genomes may contain some errors of different nature, e.g. missing genes, incorrect exon-intron structures, 'chimeras', which fuse 2 or more real genes or alternatively splitting some real genes into 2 or more models. The main premise behind the comparative modeling approach is that for closely related genomes most orthologous families have the same conserved gene structure. The algorithm maps all gene models predicted in each individual Aspergillus genome to the other genomes and, for each locus, selects from potentially many competing models, the one whichmore » most closely resembles the orthologous genes from other genomes. This procedure is iterated until no further change in gene models is observed. For Aspergillus genomes we predicted in total 4503 new gene models ( ~;;2percent per genome), supported by comparative analysis, additionally correcting ~;;18percent of old gene models. This resulted in a total of 4065 more genes with annotated PFAM domains (~;;3percent increase per genome). Analysis of a few genomes with EST/transcriptomics data shows that the new annotation sets also have a higher number of EST-supported splice sites at exon-intron boundaries.« less

Simulating Halos with the Caterpillar Project

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2016-04-01

The Caterpillar Project is a beautiful series of high-resolution cosmological simulations. The goal of this project is to examine the evolution of dark-matter halos like the Milky Ways, to learn about how galaxies like ours formed. This immense computational project is still in progress, but the Caterpillar team is already providing a look at some of its first results.Lessons from Dark-Matter HalosWhy simulate the dark-matter halos of galaxies? Observationally, the formation history of our galaxy is encoded in galactic fossil record clues, like the tidal debris from disrupted satellite galaxies in the outer reaches of our galaxy, or chemical abundance patterns throughout our galactic disk and stellar halo.But to interpret this information in a way that lets us learn about our galaxys history, we need to first test galaxy formation and evolution scenarios via cosmological simulations. Then we can compare the end result of these simulations to what we observe today.This figure illustrates the difference that mass resolution makes. In the left panel, the mass resolution is 1.5*10^7 solar masses per particle. In the right panel, the mass resolution is 3*10^4 solar masses per particle [Griffen et al. 2016]A Computational ChallengeDue to how computationally expensive such simulations are, previous N-body simulations of the growth of Milky-Way-like halos have consisted of only one or a few halos each. But in order to establish a statistical understanding of how galaxy halos form and find out whether the Milky Ways halo is typical or unusual! it is necessary to simulate a larger number of halos.In addition, in order to accurately follow the formation and evolution of substructure within the dark-matter halos, these simulations must be able to resolve the smallest dwarf galaxies, which are around a million solar masses. This requires an extremely high mass resolution, which adds to the computational expense of the simulation.First OutcomesThese are the challenges faced by

HaloSat- A CubeSat to Study the Hot Galactic Halo

NASA Astrophysics Data System (ADS)

Kaaret, Philip

We propose to develop, build, and fly HaloSat, a CubeSat capable of measuring the oxygen line emission from the hot Galactic halo. A dedicated CubeSat enables an instrument design and observing strategy to maximize the halo signal while minimizing foregrounds from solar wind charge exchange interactions within the solar system. We will use HaloSat to map the distribution of hot gas in the Milky Way and determine whether it fills an extended, and thus massive halo, or whether the halo is compact, and thus does not contribute significantly to the total mass of the Milky Way. HaloSat can be accomplished at modest cost using a CubeSat, a novel platform for space astrophysics missions. We will use a commercially available CubeSat bus and commercially available X-ray detectors to reduce development risk and minimize overall mission cost. HaloSat builds on the initiatives of GSFC/Wallops Flight Facility (WFF) in the development of CubeSats for low cost access to space and relies on the technical expertise of WFF personnel for spacecraft and mission design and operations. The team, from University of Iowa (UI), GSFC, Johns Hopkins, and CNRS (France), contains experts in X-ray detector development and data analysis and the astrophysics of hot plasmas and Galactic structure. The UI team will include a number of junior researchers (undergraduates, graduate students, and a postdoc) and help train them for future leadership roles on NASA space flight missions.

Cold dark matter. 1: The formation of dark halos

NASA Technical Reports Server (NTRS)

Gelb, James M.; Bertschinger, Edmund

1994-01-01

We use numerical simulations of critically closed cold dark matter (CDM) models to study the effects of numerical resolution on observable quantities. We study simulations with up to 256(exp 3) particles using the particle-mesh (PM) method and with up to 144(exp 3) particles using the adaptive particle-particle-mesh (P3M) method. Comparisons of galaxy halo distributions are made among the various simulations. We also compare distributions with observations, and we explore methods for identifying halos, including a new algorithm that finds all particles within closed contours of the smoothed density field surrounding a peak. The simulated halos show more substructure than predicted by the Press-Schechter theory. We are able to rule out all omega = 1 CDM models for linear amplitude sigma(sub 8) greater than or approximately = 0.5 because the simulations produce too many massive halos compared with the observations. The simulations also produce too many low-mass halos. The distribution of halos characterized by their circular velocities for the P3M simulations is in reasonable agreement with the observations for 150 km/s less than or = V(sub circ) less than or = 350 km/s.

Diverse stellar haloes in nearby Milky Way mass disc galaxies

NASA Astrophysics Data System (ADS)

Harmsen, Benjamin; Monachesi, Antonela; Bell, Eric F.; de Jong, Roelof S.; Bailin, Jeremy; Radburn-Smith, David J.; Holwerda, Benne W.

2017-04-01

We have examined the resolved stellar populations at large galactocentric distances along the minor axis (from 10 kpc up to between 40 and 75 kpc), with limited major axis coverage, of six nearby highly inclined Milky Way (MW) mass disc galaxies using Hubble Space Telescope data from the Galaxy haloes, Outer discs, Substructure, Thick discs, and Star clusters (GHOSTS) survey. We select red giant branch stars to derive stellar halo density profiles. The projected minor axis density profiles can be approximated by power laws with projected slopes of -2 to -3.7 and a diversity of stellar halo masses of 1-6 × 109 M⊙, or 2-14 per cent of the total galaxy stellar masses. The typical intrinsic scatter around a smooth power-law fit is 0.05-0.1 dex owing to substructure. By comparing the minor and major axis profiles, we infer projected axis ratios c/a at ˜25 kpc between 0.4and0.75. The GHOSTS stellar haloes are diverse, lying between the extremes charted out by the (rather atypical) haloes of the MW and M31. We find a strong correlation between the stellar halo metallicities and the stellar halo masses. We compare our results with cosmological models, finding good agreement between our observations and accretion-only models where the stellar haloes are formed by the disruption of dwarf satellites. In particular, the strong observed correlation between stellar halo metallicity and mass is naturally reproduced. Low-resolution hydrodynamical models have unrealistically high stellar halo masses. Current high-resolution hydrodynamical models appear to predict stellar halo masses somewhat higher than observed but with reasonable metallicities, metallicity gradients, and density profiles.

The Milky Way, the Galactic halo, and the Halos of Galaxies

NASA Astrophysics Data System (ADS)

Gerhard, Ortwin

2015-08-01

The Milky Way, "our" Galaxy, is currently the subject of intense study with many ground-based surveys, in anticipation of upcoming results from the GAIA mission. From this work we have been learning about the full three-dimensional structure of the Galactic box/peanut bulge, the distribution of stars in the bar and disk, and the many streams in the Galactic halo. The data tell us that most of the Galactic bulge formed from the disk, and that a large fraction of the Galactic halo has been accreted from outside. Similarly, in many external galaxy halos there is now evidence for tidal streams and accretion of satellites. To see these features requires exquisite data - mostly very deep photometry, but some halo substructures have also been found with kinematic data. These observations illustrate how galaxy halos are still growing, and sometimes can be used to "time" the accretion events. In comparison with cosmological simulations, the structure of galaxy halos gives us a vivid illustration of the hierarchical nature of our Universe.

Galaxy and Mass Assembly (GAMA): halo formation times and halo assembly bias on the cosmic web

NASA Astrophysics Data System (ADS)

Tojeiro, Rita; Eardley, Elizabeth; Peacock, John A.; Norberg, Peder; Alpaslan, Mehmet; Driver, Simon P.; Henriques, Bruno; Hopkins, Andrew M.; Kafle, Prajwal R.; Robotham, Aaron S. G.; Thomas, Peter; Tonini, Chiara; Wild, Vivienne

2017-09-01

We present evidence for halo assembly bias as a function of geometric environment (GE). By classifying Galaxy and Mass Assembly (GAMA) galaxy groups as residing in voids, sheets, filaments or knots using a tidal tensor method, we find that low-mass haloes that reside in knots are older than haloes of the same mass that reside in voids. This result provides direct support to theories that link strong halo tidal interactions with halo assembly times. The trend with GE is reversed at large halo mass, with haloes in knots being younger than haloes of the same mass in voids. We find a clear signal of halo downsizing - more massive haloes host galaxies that assembled their stars earlier. This overall trend holds independently of GE. We support our analysis with an in-depth exploration of the L-Galaxies semi-analytic model, used here to correlate several galaxy properties with three different definitions of halo formation time. We find a complex relationship between halo formation time and galaxy properties, with significant scatter. We confirm that stellar mass to halo mass ratio, specific star formation rate (SFR) and mass-weighed age are reasonable proxies of halo formation time, especially at low halo masses. Instantaneous SFR is a poor indicator at all halo masses. Using the same semi-analytic model, we create mock spectral observations using complex star formation and chemical enrichment histories, which approximately mimic GAMA's typical signal-to-noise ratio and wavelength range. We use these mocks to assert how well potential proxies of halo formation time may be recovered from GAMA-like spectroscopic data.

On the scatter in the relation between stellar mass and halo mass: random or halo formation time dependent?

NASA Astrophysics Data System (ADS)

Wang, Lan; De Lucia, Gabriella; Weinmann, Simone M.

2013-05-01

The empirical traditional halo occupation distribution (HOD) model of Wang et al. fits, by construction, both the stellar mass function and correlation function of galaxies in the local Universe. In contrast, the semi-analytical models of De Lucia & Blazoit (hereafter DLB07) and Guo et al. (hereafter Guo11), built on the same dark matter halo merger trees than the empirical model, still have difficulties in reproducing these observational data simultaneously. We compare the relations between the stellar mass of galaxies and their host halo mass in the three models, and find that they are different. When the relations are rescaled to have the same median values and the same scatter as in Wang et al., the rescaled DLB07 model can fit both the measured galaxy stellar mass function and the correlation function measured in different galaxy stellar mass bins. In contrast, the rescaled Guo11 model still overpredicts the clustering of low-mass galaxies. This indicates that the detail of how galaxies populate the scatter in the stellar mass-halo mass relation does play an important role in determining the correlation functions of galaxies. While the stellar mass of galaxies in the Wang et al. model depends only on halo mass and is randomly distributed within the scatter, galaxy stellar mass depends also on the halo formation time in semi-analytical models. At fixed value of infall mass, galaxies that lie above the median stellar mass-halo mass relation reside in haloes that formed earlier, while galaxies that lie below the median relation reside in haloes that formed later. This effect is much stronger in Guo11 than in DLB07, which explains the overclustering of low mass galaxies in Guo11. Assembly bias in Guo11 model might be overly strong. Nevertheless, in case that a significant assembly bias indeed exists in the real Universe, one needs to use caution when applying current HOD and abundance matching models that employ the assumption of random scatter in the relation

Plant Comparative and Functional Genomics

DOE PAGES

Yang, Xiaohan; Leebens-Mack, Jim; Chen, Feng; ...

2015-01-01

Plants form the foundation for our global ecosystem and are essential for environmental and human health. An increasing number of available plant genomes and tractable experimental systems, comparative and functional plant genomics research is greatly expanding our knowledge of the molecular basis of economically and nutritionally important traits in crop plants. Inferences drawn from comparative genomics are motivating experimental investigations of gene function and gene interactions. In this special issue aims to highlight recent advances made in comparative and functional genomics research in plants. Nine original research articles in this special issue cover five important topics: (1) transcription factor genemore » families relevant to abiotic stress tolerance; (2) plant secondary metabolism; (3) transcriptomebased markers for quantitative trait locus; (4) epigenetic modifications in plant-microbe interactions; and (5) computational prediction of protein-protein interactions. Finally, we studied the plant species in these articles which include model species as well as nonmodel plant species of economic importance (e.g., food crops and medicinal plants).« less

Plant Comparative and Functional Genomics

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

Yang, Xiaohan; Leebens-Mack, Jim; Chen, Feng

Plants form the foundation for our global ecosystem and are essential for environmental and human health. An increasing number of available plant genomes and tractable experimental systems, comparative and functional plant genomics research is greatly expanding our knowledge of the molecular basis of economically and nutritionally important traits in crop plants. Inferences drawn from comparative genomics are motivating experimental investigations of gene function and gene interactions. In this special issue aims to highlight recent advances made in comparative and functional genomics research in plants. Nine original research articles in this special issue cover five important topics: (1) transcription factor genemore » families relevant to abiotic stress tolerance; (2) plant secondary metabolism; (3) transcriptomebased markers for quantitative trait locus; (4) epigenetic modifications in plant-microbe interactions; and (5) computational prediction of protein-protein interactions. Finally, we studied the plant species in these articles which include model species as well as nonmodel plant species of economic importance (e.g., food crops and medicinal plants).« less

Galactic Warps in Triaxial Halos

NASA Astrophysics Data System (ADS)

Jeon, Myoungwon; Kim, Sungsoo S.; Ann, Hong Bae

2009-05-01

We study the behavior of galactic disks in triaxial halos both numerically and analytically to see if warps can be excited and sustained in triaxial potentials. We consider the following two scenarios: (1) galactic disks that are initially tilted relative to the equatorial plane of the halo (for a pedagogical purpose), and (2) tilted infall of dark matter relative to the equatorial plane of the disk and the halo. With numerical simulations of 100,000 disk particles in a fixed halo potential, we find that in triaxial halos, warps can be excited and sustained just as in spherical or axisymmetric halos but they show some oscillatory behavior and even can be transformed to a polar-ring system if the halo has a prolate-like triaxiality. The nonaxisymmetric component of the halo causes the disk to nutate, and the differential nutation between the inner and outer parts of the disk generally makes the magnitude of the warp slightly diminish and fluctuate. We also find that warps are relatively weaker in oblate and oblate-like triaxial halos, and since these halos are the halo configurations of disk galaxies inferred by cosmological simulations, our results are consistent with the fact that most of the observed warps are quite weak. We derive approximate formulae for the torques exerted on the disk by the triaxial halo and the dark matter torus, and with these formulae we successfully describe the behavior of the disks in our simulations. The techniques used in deriving these formulae could be applied for realistic halos with more complex structures.

The Prolate Dark Matter Halo of the Andromeda Galaxy

NASA Astrophysics Data System (ADS)

Hayashi, Kohei; Chiba, Masashi

2014-07-01

We present new limits on the global shape of the dark matter halo in the Andromeda galaxy using and generalizing non-spherical mass models developed by Hayashi & Chiba and compare our results with theoretical predictions of cold dark matter (CDM) models. This is motivated by the fact that CDM models predict non-spherical virialized dark halos, which reflect the process of mass assembly in the galactic scale. Applying our models to the latest kinematic data of globular clusters and dwarf spheroidal galaxies in the Andromeda halo, we find that the most plausible cases for Andromeda yield a prolate shape for its dark halo, irrespective of assumed density profiles. We also find that this prolate dark halo in Andromeda is consistent with theoretical predictions in which the satellites are distributed anisotropically and preferentially located along major axes of their host halos. It is a reflection of the intimate connection between galactic dark matter halos and the cosmic web. Therefore, our result is profound in understanding internal dynamics of halo tracers in Andromeda, such as orbital evolutions of tidal stellar streams, which play important roles in extracting the abundance of CDM subhalos through their dynamical effects on stream structures.

Comparative primate genomics: emerging patterns of genome content and dynamics

PubMed Central

Rogers, Jeffrey; Gibbs, Richard A.

2014-01-01

Preface Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for several primates, with analyses of several others underway. Whole genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other nonhuman primates provide valuable insight into genetic similarities and differences among species used as models for disease-related research. This review summarizes current knowledge regarding primate genome content and dynamics and offers a series of goals for the near future. PMID:24709753

Comparative primate genomics: emerging patterns of genome content and dynamics.

PubMed

Rogers, Jeffrey; Gibbs, Richard A

2014-05-01

Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for various primate species, and analyses of several others are underway. Whole-genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other non-human primates offer valuable insights into genetic similarities and differences among species that are used as models for disease-related research. This Review summarizes current knowledge regarding primate genome content and dynamics, and proposes a series of goals for the near future.

The Milky Way, the Galactic Halo, and the Halos of Galaxies

NASA Astrophysics Data System (ADS)

Gerhard, Ortwin

2016-08-01

The Milky Way, ``our'' Galaxy, is currently the subject of intense study with many ground-based surveys, in anticipation of upcoming results from the Gaia mission. From this work we have been learning about the full three-dimensional structure of the Galactic box/peanut bulge, the distribution of stars in the bar and disk, and the many streams and substructures in the Galactic halo. The data indicate that a large fraction of the Galactic halo has been accreted from outside. Similarly, in many external galaxy halos there is now evidence for tidal streams and accretion of satellites. To study these features requires exquisite, deep photometry and spectroscopy. These observations illustrate how galaxy halos are still growing, and sometimes can be used to ``time'' the accretion events. In comparison with cosmological simulations, the structure of galaxy halos gives us a vivid illustration of the hierarchical nature of our Universe.

HALOE Science Investigation

NASA Technical Reports Server (NTRS)

Benner, D. Chris

1998-01-01

This cooperative agreement has investigated a number of spectroscopic problems of interest to the Halogen Occultation Experiment (HALOE). The types of studies performed are in two parts, namely, those that involve the testing and characterization of correlation spectrometers and those that provide basic molecular spectroscopic information. In addition, some solar studies were performed with the calibration data returned by HALOE from orbit. In order to accomplish this a software package was written as part of this cooperative agreement. The HALOE spectroscopic instrument package was used in various tests of the HALOE flight instrument. These included the spectral response test, the early stages of the gas response test and various spectral response tests of the detectors and optical elements of the instruments. Considerable effort was also expended upon the proper laboratory setup for many of the prelaunch tests of the HALOE flight instrument, including the spectral response test and the gas response test. These tests provided the calibration and the assurance that the calibration was performed correctly.

Statistical Aspects of X-Class Halo and Non-Halo Events, 1996-2014

NASA Technical Reports Server (NTRS)

Wilson, Robert M.

2016-01-01

Of the 166 X-class events that occurred during the interval 1996-2014, 80 had associations with halo events, 68 had no associations with halo events, and 18 occurred during LASCO (Large Angle and Spectrometric COronagraph) data gaps. Both the duration and location of the X-class halo events proved to be statistically important parameters with respect to the geo-effectiveness of the events. Forty-four of the 80 X-class halo events occurred within 45 degrees of the Sun's central meridian and 47 of the 80 had duration greater than or equal to 30 minutes, whereas only 28 of the 68 X-class non-halo events occurred within 45 degrees of the Sun's central meridian (2 events have unknown location) and 22 of the 68 had duration greater than or equal to 30 minutes. Ignoring the 4 largest X-class flares greater than or equal to X4.0 during the LASCO data gaps, 17 of the remaining 20 were associated with halo events, and 14 of the 17 had at least one geo-magnetically disturbed day (Ap (i.e. NOAA's Ap* (ApStar)index: the major magnetic storms going back to 1932) greater than or equal to 25 nanotesias) within 1-5 days following the X-class halo event. Based on the hourly Dst (Disturbance storm time) index, the most geo-effective X-class halo event during the interval 1996-2014 was that of an X1.7 flare that occurred on 2001 March 29 at 0957, having an hourly Disturbance storm time minimum equal to minus 387 nanotesias. On average, the X-class halo events (80 events) were found to have a mean duration (42 minutes) slightly longer than the mean duration (29 minutes) of the X-class non-halo events (68 events) with the difference in the means being statistically important at the 1 percent level of significance.

On physical scales of dark matter halos

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

Zemp, Marcel, E-mail: mzemp@pku.edu.cn

2014-09-10

It is common practice to describe formal size and mass scales of dark matter halos as spherical overdensities with respect to an evolving density threshold. Here, we critically investigate the evolutionary effects of several such commonly used definitions and compare them to the halo evolution within fixed physical scales as well as to the evolution of other intrinsic physical properties of dark matter halos. It is shown that, in general, the traditional way of characterizing sizes and masses of halos dramatically overpredicts the degree of evolution in the last 10 Gyr, especially for low-mass halos. This pseudo-evolution leads to themore » illusion of growth even though there are no major changes within fixed physical scales. Such formal size definitions also serve as proxies for the virialized region of a halo in the literature. In general, those spherical overdensity scales do not coincide with the virialized region. A physically more precise nomenclature would be to simply characterize them by their very definition instead of calling such formal size and mass definitions 'virial'. In general, we find a discrepancy between the evolution of the underlying physical structure of dark matter halos seen in cosmological structure formation simulations and pseudo-evolving formal virial quantities. We question the importance of the role of formal virial quantities currently ubiquitously used in descriptions, models, and relations that involve properties of dark matter structures. Concepts and relations based on pseudo-evolving formal virial quantities do not properly reflect the actual evolution of dark matter halos and lead to an inaccurate picture of the physical evolution of our universe.« less

Substructure of fuzzy dark matter haloes

NASA Astrophysics Data System (ADS)

Du, Xiaolong; Behrens, Christoph; Niemeyer, Jens C.

2017-02-01

We derive the halo mass function (HMF) for fuzzy dark matter (FDM) by solving the excursion set problem explicitly with a mass-dependent barrier function, which has not been done before. We find that compared to the naive approach of the Sheth-Tormen HMF for FDM, our approach has a higher cutoff mass and the cutoff mass changes less strongly with redshifts. Using merger trees constructed with a modified version of the Lacey & Cole formalism that accounts for suppressed small-scale power and the scale-dependent growth of FDM haloes and the semi-analytic GALACTICUS code, we study the statistics of halo substructure including the effects from dynamical friction and tidal stripping. We find that if the dark matter is a mixture of cold dark matter (CDM) and FDM, there will be a suppression on the halo substructure on small scales which may be able to solve the missing satellites problem faced by the pure CDM model. The suppression becomes stronger with increasing FDM fraction or decreasing FDM mass. Thus, it may be used to constrain the FDM model.

The prolate dark matter halo of the Andromeda galaxy

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

Hayashi, Kohei; Chiba, Masashi, E-mail: k.hayasi@astr.tohoku.ac.jp, E-mail: chiba@astr.tohoku.ac.jp

We present new limits on the global shape of the dark matter halo in the Andromeda galaxy using and generalizing non-spherical mass models developed by Hayashi and Chiba and compare our results with theoretical predictions of cold dark matter (CDM) models. This is motivated by the fact that CDM models predict non-spherical virialized dark halos, which reflect the process of mass assembly in the galactic scale. Applying our models to the latest kinematic data of globular clusters and dwarf spheroidal galaxies in the Andromeda halo, we find that the most plausible cases for Andromeda yield a prolate shape for itsmore » dark halo, irrespective of assumed density profiles. We also find that this prolate dark halo in Andromeda is consistent with theoretical predictions in which the satellites are distributed anisotropically and preferentially located along major axes of their host halos. It is a reflection of the intimate connection between galactic dark matter halos and the cosmic web. Therefore, our result is profound in understanding internal dynamics of halo tracers in Andromeda, such as orbital evolutions of tidal stellar streams, which play important roles in extracting the abundance of CDM subhalos through their dynamical effects on stream structures.« less

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline.

PubMed

Agrawal, Sonia; Arze, Cesar; Adkins, Ricky S; Crabtree, Jonathan; Riley, David; Vangala, Mahesh; Galens, Kevin; Fraser, Claire M; Tettelin, Hervé; White, Owen; Angiuoli, Samuel V; Mahurkar, Anup; Fricke, W Florian

2017-04-27

The benefit of increasing genomic sequence data to the scientific community depends on easy-to-use, scalable bioinformatics support. CloVR-Comparative combines commonly used bioinformatics tools into an intuitive, automated, and cloud-enabled analysis pipeline for comparative microbial genomics. CloVR-Comparative runs on annotated complete or draft genome sequences that are uploaded by the user or selected via a taxonomic tree-based user interface and downloaded from NCBI. CloVR-Comparative runs reference-free multiple whole-genome alignments to determine unique, shared and core coding sequences (CDSs) and single nucleotide polymorphisms (SNPs). Output includes short summary reports and detailed text-based results files, graphical visualizations (phylogenetic trees, circular figures), and a database file linked to the Sybil comparative genome browser. Data up- and download, pipeline configuration and monitoring, and access to Sybil are managed through CloVR-Comparative web interface. CloVR-Comparative and Sybil are distributed as part of the CloVR virtual appliance, which runs on local computers or the Amazon EC2 cloud. Representative datasets (e.g. 40 draft and complete Escherichia coli genomes) are processed in <36 h on a local desktop or at a cost of <$20 on EC2. CloVR-Comparative allows anybody with Internet access to run comparative genomics projects, while eliminating the need for on-site computational resources and expertise.

Cosmic web type dependence of halo clustering

NASA Astrophysics Data System (ADS)

Fisher, J. D.; Faltenbacher, A.

2018-01-01

We use the Millennium Simulation to show that halo clustering varies significantly with cosmic web type. Haloes are classified as node, filament, sheet and void haloes based on the eigenvalue decomposition of the velocity shear tensor. The velocity field is sampled by the peculiar velocities of a fixed number of neighbouring haloes, and spatial derivatives are computed using a kernel borrowed from smoothed particle hydrodynamics. The classification scheme is used to examine the clustering of haloes as a function of web type for haloes with masses larger than 1011 h- 1 M⊙. We find that node haloes show positive bias, filament haloes show negligible bias and void and sheet haloes are antibiased independent of halo mass. Our findings suggest that the mass dependence of halo clustering is rooted in the composition of web types as a function of halo mass. The substantial fraction of node-type haloes for halo masses ≳ 2 × 1013 h- 1 M⊙ leads to positive bias. Filament-type haloes prevail at intermediate masses, 1012-1013 h- 1 M⊙, resulting in unbiased clustering. The large contribution of sheet-type haloes at low halo masses ≲ 1012 h- 1 M⊙ generates antibiasing.

Lithium in halo stars from standard stellar evolution

NASA Technical Reports Server (NTRS)

Deliyannis, Constantine P.; Demarque, Pierre; Kawaler, Steven D.

1990-01-01

A grid has been constructed of theoretical evolution sequences of models for low-metallicity stars from the premain-sequence to the giant branch phases. The grid is used to study the history of surface Li abundance during standard stellar evolution. The Li-7 observations of halo stars by Spite and Spite (1982) and subsequent observations are synthesized to separate the halo stars by age. The theory of surface Li abundance is illustrated by following the evolution of a reference halo star model from the contracting fully convective premain sequence to the giant branch phase. The theoretical models are compared with observed Li abundances. The results show that the halo star lithium abundances can be explained in the context of standard stellar evolution theory using completely standard assumptions and physics.

"Invisible" Galactic Halos.

ERIC Educational Resources Information Center

Lugt, Karel Vander

1993-01-01

Develops a simple core-halo model of a galaxy that exhibits the main features of observed rotation curves and quantitatively illustrates the need to postulate halos of dark matter. Uses only elementary mechanics. (Author/MVL)

Comparative Genomics of the Cucurbitaceae

USDA-ARS?s Scientific Manuscript database

The genome size for watermelon, melon, cucumber, and pumpkin is 425, 454, 367, and 502 Mbp, respectively, and considered medium size as compared with most other crops. Whole-genome duplication is common in angiosperm plants. Research has revealed a paleohexaploidy (') event in the common ancestor of...

Ebolavirus comparative genomics

PubMed Central

Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat; Uberbacher, Edward C.; Land, Miriam; Zhang, Qian; Wanchai, Visanu; Chai, Juanjuan; Nielsen, Morten; Trolle, Thomas; Lund, Ole; Buzard, Gregory S.; Pedersen, Thomas D.; Wassenaar, Trudy M.; Ussery, David W.

2015-01-01

The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms a distinct group from all other sequenced viral genomes. All filovirus genomes sequenced to date encode proteins with similar functions and gene order, although there is considerable divergence in sequences between the three genera Ebolavirus, Cuevavirus and Marburgvirus within the family Filoviridae. Whereas all ebolavirus genomes are quite similar (multiple sequences of the same strain are often identical), variation is most common in the intergenic regions and within specific areas of the genes encoding the glycoprotein (GP), nucleoprotein (NP) and polymerase (L). We predict regions that could contain epitope-binding sites, which might be good vaccine targets. This information, combined with glycosylation sites and experimentally determined epitopes, can identify the most promising regions for the development of therapeutic strategies. This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan). PMID:26175035

Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus

PubMed Central

Sharma, Gaurav; Narwani, Tarun; Subramanian, Srikrishna

2016-01-01

Myxobacteria, a group of Gram-negative aerobes, belong to the class δ-proteobacteria and order Myxococcales. Unlike anaerobic δ-proteobacteria, they exhibit several unusual physiogenomic properties like gliding motility, desiccation-resistant myxospores and large genomes with high coding density. Here we report a 9.5 Mbp complete genome of Myxococcus hansupus that encodes 7,753 proteins. Phylogenomic and genome-genome distance based analysis suggest that Myxococcus hansupus is a novel member of the genus Myxococcus. Comparative genome analysis with other members of the genus Myxococcus was performed to explore their genome diversity. The variation in number of unique proteins observed across different species is suggestive of diversity at the genus level while the overrepresentation of several Pfam families indicates the extent and mode of genome expansion as compared to non-Myxococcales δ-proteobacteria. PMID:26900859

Ensembl 2002: accommodating comparative genomics.

PubMed

Clamp, M; Andrews, D; Barker, D; Bevan, P; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Hubbard, T; Kasprzyk, A; Keefe, D; Lehvaslaiho, H; Iyer, V; Melsopp, C; Mongin, E; Pettett, R; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Birney, E

2003-01-01

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

[Halos and multifocal intraocular lenses: origin and interpretation].

PubMed

Alba-Bueno, F; Vega, F; Millán, M S

2014-10-01

To present the theoretical and experimental characterization of the halo in multifocal intraocular lenses (MIOL). The origin of the halo in a MIOL is the overlaying of 2 or more images. Using geometrical optics, it can be demonstrated that the diameter of each halo depends on the addition of the lens (ΔP), the base power (P(d)), and the diameter of the IOL that contributes to the «non-focused» focus. In the image plane that corresponds to the distance focus, the halo diameter (δH(d)) is given by: δH(d)=d(pn) ΔP/P(d), where d(pn) is the diameter of the IOL that contributes to the near focus. Analogously, in the near image plane the halo diameter (δH(n)) is: δH(n)=d(pd) ΔP/P(d), where d(pd) is the diameter of the IOL that contributes to the distance focus. Patients perceive halos when they see bright objects over a relatively dark background. In vitro, the halo can be characterized by analyzing the intensity profile of the image of a pinhole that is focused by each of the foci of a MIOL. A comparison has been made between the halos induced by different MIOL of the same base power (20D) in an optical bench. As predicted by theory, the larger the addition of the MIOL, the larger the halo diameter. For large pupils and with MIOL with similar aspheric designs and addition (SN6AD3 vs ZMA00), the apodized MIOL has a smaller halo diameter than a non-apodized one in distance vision, while in near vision the size is very similar, but the relative intensity is higher in the apodized MIOL. When comparing lenses with the same diffractive design, but with different spherical-aspheric base design (SN60D3 vs SN6AD3), the halo in distance vision of the spherical MIOL is larger, while in near vision the spherical IOL induces a smaller halo, but with higher intensity due to the spherical aberration of the distance focus in the near image. In the case of a trifocal-diffractive IOL (AT LISA 839MP) the most noticeable characteristic is the double-halo formation due to the 2 non

Galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation

NASA Astrophysics Data System (ADS)

Chisari, N. E.; Koukoufilippas, N.; Jindal, A.; Peirani, S.; Beckmann, R. S.; Codis, S.; Devriendt, J.; Miller, L.; Dubois, Y.; Laigle, C.; Slyz, A.; Pichon, C.

2017-11-01

Intrinsic alignments of galaxies are a significant astrophysical systematic affecting cosmological constraints from weak gravitational lensing. Obtaining numerical predictions from hydrodynamical simulations of expected survey volumes is expensive, and a cheaper alternative relies on populating large dark matter-only simulations with accurate models of alignments calibrated on smaller hydrodynamical runs. This requires connecting the shapes and orientations of galaxies to those of dark matter haloes and to the large-scale structure. In this paper, we characterize galaxy-halo alignments in the Horizon-AGN cosmological hydrodynamical simulation. We compare the shapes and orientations of galaxies in the redshift range of 0 < z < 3 to those of their embedding dark matter haloes, and to the matching haloes of a twin dark-matter only run with identical initial conditions. We find that galaxy ellipticities, in general, cannot be predicted directly from halo ellipticities. The mean misalignment angle between the minor axis of a galaxy and its embedding halo is a function of halo mass, with residuals arising from the dependence of alignment on galaxy type, but not on environment. Haloes are much more strongly aligned among themselves than galaxies, and they decrease their alignment towards low redshift. Galaxy alignments compete with this effect, as galaxies tend to increase their alignment with haloes towards low redshift. We discuss the implications of these results for current halo models of intrinsic alignments and suggest several avenues for improvement.

Spatial clustering of dark matter haloes: secondary bias, neighbour bias, and the influence of massive neighbours on halo properties

NASA Astrophysics Data System (ADS)

Salcedo, Andrés N.; Maller, Ariyeh H.; Berlind, Andreas A.; Sinha, Manodeep; McBride, Cameron K.; Behroozi, Peter S.; Wechsler, Risa H.; Weinberg, David H.

2018-04-01

We explore the phenomenon commonly known as halo assembly bias, whereby dark matter haloes of the same mass are found to be more or less clustered when a second halo property is considered, for haloes in the mass range 3.7 × 1011-5.0 × 1013 h-1 M⊙. Using the Large Suite of Dark Matter Simulations (LasDamas) we consider nine commonly used halo properties and find that a clustering bias exists if haloes are binned by mass or by any other halo property. This secondary bias implies that no single halo property encompasses all the spatial clustering information of the halo population. The mean values of some halo properties depend on their halo's distance to a more massive neighbour. Halo samples selected by having high values of one of these properties therefore inherit a neighbour bias such that they are much more likely to be close to a much more massive neighbour. This neighbour bias largely accounts for the secondary bias seen in haloes binned by mass and split by concentration or age. However, haloes binned by other mass-like properties still show a secondary bias even when the neighbour bias is removed. The secondary bias of haloes selected by their spin behaves differently than that for other halo properties, suggesting that the origin of the spin bias is different than of other secondary biases.

Comparative genomic data of the Avian Phylogenomics Project.

PubMed

Zhang, Guojie; Li, Bo; Li, Cai; Gilbert, M Thomas P; Jarvis, Erich D; Wang, Jun

2014-01-01

The evolutionary relationships of modern birds are among the most challenging to understand in systematic biology and have been debated for centuries. To address this challenge, we assembled or collected the genomes of 48 avian species spanning most orders of birds, including all Neognathae and two of the five Palaeognathae orders, and used the genomes to construct a genome-scale avian phylogenetic tree and perform comparative genomics analyses (Jarvis et al. in press; Zhang et al. in press). Here we release assemblies and datasets associated with the comparative genome analyses, which include 38 newly sequenced avian genomes plus previously released or simultaneously released genomes of Chicken, Zebra finch, Turkey, Pigeon, Peregrine falcon, Duck, Budgerigar, Adelie penguin, Emperor penguin and the Medium Ground Finch. We hope that this resource will serve future efforts in phylogenomics and comparative genomics. The 38 bird genomes were sequenced using the Illumina HiSeq 2000 platform and assembled using a whole genome shotgun strategy. The 48 genomes were categorized into two groups according to the N50 scaffold size of the assemblies: a high depth group comprising 23 species sequenced at high coverage (>50X) with multiple insert size libraries resulting in N50 scaffold sizes greater than 1 Mb (except the White-throated Tinamou and Bald Eagle); and a low depth group comprising 25 species sequenced at a low coverage (~30X) with two insert size libraries resulting in an average N50 scaffold size of about 50 kb. Repetitive elements comprised 4%-22% of the bird genomes. The assembled scaffolds allowed the homology-based annotation of 13,000 ~ 17000 protein coding genes in each avian genome relative to chicken, zebra finch and human, as well as comparative and sequence conservation analyses. Here we release full genome assemblies of 38 newly sequenced avian species, link genome assembly downloads for the 7 of the remaining 10 species, and provide a guideline of

Revealing the Cosmic Web-dependent Halo Bias

NASA Astrophysics Data System (ADS)

Yang, Xiaohu; Zhang, Youcai; Lu, Tianhuan; Wang, Huiyuan; Shi, Feng; Tweed, Dylan; Li, Shijie; Luo, Wentao; Lu, Yi; Yang, Lei

2017-10-01

Halo bias is the one of the key ingredients of the halo models. It was shown at a given redshift to be only dependent, to the first order, on the halo mass. In this study, four types of cosmic web environments—clusters, filaments, sheets, and voids—are defined within a state-of-the-art high-resolution N-body simulation. Within these environments, we use both halo-dark matter cross correlation and halo-halo autocorrelation functions to probe the clustering properties of halos. The nature of the halo bias differs strongly between the four different cosmic web environments described here. With respect to the overall population, halos in clusters have significantly lower biases in the {10}11.0˜ {10}13.5 {h}-1 {M}⊙ mass range. In other environments, however, halos show extremely enhanced biases up to a factor 10 in voids for halos of mass ˜ {10}12.0 {h}-1 {M}⊙ . Such a strong cosmic web environment dependence in the halo bias may play an important role in future cosmological and galaxy formation studies. Within this cosmic web framework, the age dependency of halo bias is found to be only significant in clusters and filaments for relatively small halos ≲ {10}12.5 {h}-1 {M}⊙ .

Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery

PubMed Central

Swain, Martin T.; Larkin, Denis M.; Caffrey, Conor R.; Davies, Stephen J.; Loukas, Alex; Skelly, Patrick J.; Hoffmann, Karl F.

2011-01-01

Schistosoma genomes provide a comprehensive resource for identifying the molecular processes that shape parasite evolution and for discovering novel chemotherapeutic or immunoprophylactic targets. Here, we demonstrate how intra- and intergenus comparative genomics can be used to drive these investigations forward, illustrate the advantages and limitations of these approaches and review how post genomic technologies offer complementary strategies for genome characterisation. While sequencing and functional characterisation of other schistosome/platyhelminth genomes continues to expedite anthelmintic discovery, we contend that future priorities should equally focus on improving assembly quality, and chromosomal assignment, of existing schistosome/platyhelminth genomes. PMID:22024648

Spatial clustering of dark matter haloes: secondary bias, neighbour bias, and the influence of massive neighbours on halo properties

DOE PAGES

Salcedo, Andres N.; Maller, Ariyeh H.; Berlind, Andreas A.; ...

2018-01-15

Here, we explore the phenomenon commonly known as halo assembly bias, whereby dark matter haloes of the same mass are found to be more or less clustered when a second halo property is considered, for haloes in the mass range 3.7 × 10 11–5.0 × 10 13 h –1 M ⊙. Using the Large Suite of Dark Matter Simulations (LasDamas) we consider nine commonly used halo properties and find that a clustering bias exists if haloes are binned by mass or by any other halo property. This secondary bias implies that no single halo property encompasses all the spatial clusteringmore » information of the halo population. The mean values of some halo properties depend on their halo's distance to a more massive neighbour. Halo samples selected by having high values of one of these properties therefore inherit a neighbour bias such that they are much more likely to be close to a much more massive neighbour. This neighbour bias largely accounts for the secondary bias seen in haloes binned by mass and split by concentration or age. However, haloes binned by other mass-like properties still show a secondary bias even when the neighbour bias is removed. The secondary bias of haloes selected by their spin behaves differently than that for other halo properties, suggesting that the origin of the spin bias is different than of other secondary biases.« less

Spatial clustering of dark matter haloes: secondary bias, neighbour bias, and the influence of massive neighbours on halo properties

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

Salcedo, Andres N.; Maller, Ariyeh H.; Berlind, Andreas A.

Here, we explore the phenomenon commonly known as halo assembly bias, whereby dark matter haloes of the same mass are found to be more or less clustered when a second halo property is considered, for haloes in the mass range 3.7 × 10 11–5.0 × 10 13 h –1 M ⊙. Using the Large Suite of Dark Matter Simulations (LasDamas) we consider nine commonly used halo properties and find that a clustering bias exists if haloes are binned by mass or by any other halo property. This secondary bias implies that no single halo property encompasses all the spatial clusteringmore » information of the halo population. The mean values of some halo properties depend on their halo's distance to a more massive neighbour. Halo samples selected by having high values of one of these properties therefore inherit a neighbour bias such that they are much more likely to be close to a much more massive neighbour. This neighbour bias largely accounts for the secondary bias seen in haloes binned by mass and split by concentration or age. However, haloes binned by other mass-like properties still show a secondary bias even when the neighbour bias is removed. The secondary bias of haloes selected by their spin behaves differently than that for other halo properties, suggesting that the origin of the spin bias is different than of other secondary biases.« less

Testing feedback-modified dark matter haloes with galaxy rotation curves: estimation of halo parameters and consistency with ΛCDM scaling relations

NASA Astrophysics Data System (ADS)

Katz, Harley; Lelli, Federico; McGaugh, Stacy S.; Di Cintio, Arianna; Brook, Chris B.; Schombert, James M.

2017-04-01

Cosmological N-body simulations predict dark matter (DM) haloes with steep central cusps (e.g. NFW). This contradicts observations of gas kinematics in low-mass galaxies that imply the existence of shallow DM cores. Baryonic processes such as adiabatic contraction and gas outflows can, in principle, alter the initial DM density profile, yet their relative contributions to the halo transformation remain uncertain. Recent high-resolution, cosmological hydrodynamic simulations by Di Cintio et al. (DC14) predict that inner density profiles depend systematically on the ratio of stellar-to-DM mass (M*/Mhalo). Using a Markov Chain Monte Carlo approach, we test the NFW and the M*/Mhalo-dependent DC14 halo models against a sample of 147 galaxy rotation curves from the new Spitzer Photometry and Accurate Rotation Curves data set. These galaxies all have extended H I rotation curves from radio interferometry as well as accurate stellar-mass-density profiles from near-infrared photometry. The DC14 halo profile provides markedly better fits to the data compared to the NFW profile. Unlike NFW, the DC14 halo parameters found in our rotation-curve fits naturally fall within two standard deviations of the mass-concentration relation predicted by Λ cold dark matter (ΛCDM) and the stellar mass-halo mass relation inferred from abundance matching with few outliers. Halo profiles modified by baryonic processes are therefore more consistent with expectations from ΛCDM cosmology and provide better fits to galaxy rotation curves across a wide range of galaxy properties than do halo models that neglect baryonic physics. Our results offer a solution to the decade long cusp-core discrepancy.

MicroScope: a platform for microbial genome annotation and comparative genomics

PubMed Central

Vallenet, D.; Engelen, S.; Mornico, D.; Cruveiller, S.; Fleury, L.; Lajus, A.; Rouy, Z.; Roche, D.; Salvignol, G.; Scarpelli, C.; Médigue, C.

2009-01-01

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope’s rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of

MicroScope: a platform for microbial genome annotation and comparative genomics.

PubMed

Vallenet, D; Engelen, S; Mornico, D; Cruveiller, S; Fleury, L; Lajus, A; Rouy, Z; Roche, D; Salvignol, G; Scarpelli, C; Médigue, C

2009-01-01

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of

Comparative Genome Analysis of Enterobacter cloacae

PubMed Central

Liu, Wing-Yee; Wong, Chi-Fat; Chung, Karl Ming-Kar; Jiang, Jing-Wei; Leung, Frederick Chi-Ching

2013-01-01

The Enterobacter cloacae species includes an extremely diverse group of bacteria that are associated with plants, soil and humans. Publication of the complete genome sequence of the plant growth-promoting endophytic E. cloacae subsp. cloacae ENHKU01 provided an opportunity to perform the first comparative genome analysis between strains of this dynamic species. Examination of the pan-genome of E. cloacae showed that the conserved core genome retains the general physiological and survival genes of the species, while genomic factors in plasmids and variable regions determine the virulence of the human pathogenic E. cloacae strain; additionally, the diversity of fimbriae contributes to variation in colonization and host determination of different E. cloacae strains. Comparative genome analysis further illustrated that E. cloacae strains possess multiple mechanisms for antagonistic action against other microorganisms, which involve the production of siderophores and various antimicrobial compounds, such as bacteriocins, chitinases and antibiotic resistance proteins. The presence of Type VI secretion systems is expected to provide further fitness advantages for E. cloacae in microbial competition, thus allowing it to survive in different environments. Competition assays were performed to support our observations in genomic analysis, where E. cloacae subsp. cloacae ENHKU01 demonstrated antagonistic activities against a wide range of plant pathogenic fungal and bacterial species. PMID:24069314

Sun-Earth L1 Region Halo-To-Halo Orbit and Halo-To-LisaJous Orbit Transfers

NASA Technical Reports Server (NTRS)

Roberts, Craig E.; DeFazio, Robert

2004-01-01

Practical techniques for designing transfer trajectories between Libration Point Orbits (LPOs) are presented. Motivation for development of these techniques was provided by a hardware contingency experienced by the Solar Heliospheric Observatory (SOHO), a joint mission of the European Space Agency (ESA) and the National Aeronautics and Space Administration (NASA) orbiting the L1 point of the Sun-Earth system. A potential solution to the problem involved a transfer from SOHO s periodic halo orbit to a new LPO of substantially different dimensions. Assuming the SOHO halo orbit as the departure orbit, several practical LPO transfer techniques were developed to obtain new Lissajous or periodic halo orbits that satisfy mission requirements and constraints. While not implemented for the SOHO mission, practical LPO transfer techniques were devised that are generally applicable to current and future LPO missions.

The massive halos of spiral galaxies

NASA Technical Reports Server (NTRS)

Zaritsky, Dennis; White, Simon D. M.

1994-01-01

We use a sample of satellite galaxies to demonstrate the existence of extended massive dark halos around spiral galaxies. Isolated spirals with rotation velocities near 250 km/s have a typical halo mass within 200 kpc of 1.5-2.6 x 10(exp 12) solar mass (90% confidence range for H(sub 0) = 75 km/s/Mpc). This result is most easily derived using standard mass estimator techniques, but such techniques do not account for the strong observational selection effects in the sample, nor for the extended mass distributions that the data imply. These complications can be addressed using scale-free models similar to those previously employed to study binary galaxies. When satellite velocities are assumed isotropic, both methods imply massive and extended halos. However, the derived masses depend sensitively on the assumed shape of satellite orbits. Furthermore, both methods ignore the fact that many of the satellites in the sample have orbital periods comparable to the Hubble time. The orbital phases of such satellites cannot be random, and their distribution in radius cannot be freely adjusted; rather these properties reflect ongoing infall onto the outer halos of their primaries. We use detailed dynamical models for halo formation to evaluate these problems, and we devise a maximum likelihood technique for estimating the parameters of such models from the data. The most strongly constrained parameter is the mass within 200-300 kpc, giving the confidence limits quoted above. The eccentricity, e, of satellite orbits is also strongly constrained, 0.50 less than e less than 0.88 at 90% confidence, implying a near-isotropic distribution of satellite velocities. The cosmic density parameter in the vicinity of our isolated halos exceeds 0.13 at 90% confidence, with preferred values exceeding 0.3.

The Dual Origin Of Stellar Halos

NASA Astrophysics Data System (ADS)

Zolotov, Adi

In the dominant Lambda+Cold Dark Matter cosmological paradigm, galaxy stellar halos are thought to form hierarchically from multiple accretion events, starting from the first structures to collapse in the Universe. This dissertation aims to make the first detailed theoretical predictions for the origin of galactic stellar halos. We focus on understanding the physical processes involved in halo formation using high-resolution, N-body + Smooth Particle Hydrodynamic simulations of disk galaxies in a cosmological context. These self-consistent simulations are used to study the competing importance of dissipative processes and dissipationless mergers in the formation of stellar halos. The relative contribution of each mechanism, and its specific role in assembling the inner and outer regions of halos is explored, as a function of galaxy mass and merging history. We show that the presence of both accreted and in situ stars in halos is a generic feature of galaxy formation. For L* galaxies, the relative contribution of each stellar population to a halo is shown to be a function of a galaxy's accretion history. Galaxies with recent mergers, like M31, will host relatively few in situ stars, while galaxies with more quiescent recent histories, like the Milky Way, will likely have a larger relative contribution from an in situ population. We show that in situ halo stars are more [alpha/Fe]-rich than accreted stars at the high [Fe/H] end of a halo's metallicity distribution function. In lower mass galaxies, M ˜ 1010 M, in situ stars dominate the stellarmass of halos. In these galaxies, in situ halo stars are, on average, younger and more metal-rich than accreted halo stars. Because in situ stars are dominant, these trends result in halos that are more metal-rich than simple accretion models predict. The halos of low mass galaxies do not extend out to the virial radii of the primary, as they do in more massive galaxies. We find that the ratio of luminous-halo mass to total

Minimizing the stochasticity of halos in large-scale structure surveys

NASA Astrophysics Data System (ADS)

Hamaus, Nico; Seljak, Uroš; Desjacques, Vincent; Smith, Robert E.; Baldauf, Tobias

2010-08-01

In recent work (Seljak, Hamaus, and Desjacques 2009) it was found that weighting central halo galaxies by halo mass can significantly suppress their stochasticity relative to the dark matter, well below the Poisson model expectation. This is useful for constraining relations between galaxies and the dark matter, such as the galaxy bias, especially in situations where sampling variance errors can be eliminated. In this paper we extend this study with the goal of finding the optimal mass-dependent halo weighting. We use N-body simulations to perform a general analysis of halo stochasticity and its dependence on halo mass. We investigate the stochasticity matrix, defined as Cij≡⟨(δi-biδm)(δj-bjδm)⟩, where δm is the dark matter overdensity in Fourier space, δi the halo overdensity of the i-th halo mass bin, and bi the corresponding halo bias. In contrast to the Poisson model predictions we detect nonvanishing correlations between different mass bins. We also find the diagonal terms to be sub-Poissonian for the highest-mass halos. The diagonalization of this matrix results in one large and one low eigenvalue, with the remaining eigenvalues close to the Poisson prediction 1/n¯, where n¯ is the mean halo number density. The eigenmode with the lowest eigenvalue contains most of the information and the corresponding eigenvector provides an optimal weighting function to minimize the stochasticity between halos and dark matter. We find this optimal weighting function to match linear mass weighting at high masses, while at the low-mass end the weights approach a constant whose value depends on the low-mass cut in the halo mass function. This weighting further suppresses the stochasticity as compared to the previously explored mass weighting. Finally, we employ the halo model to derive the stochasticity matrix and the scale-dependent bias from an analytical perspective. It is remarkably successful in reproducing our numerical results and predicts that the

Halo-independent direct detection analyses without mass assumptions

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

Anderson, Adam J.; Fox, Patrick J.; Kahn, Yonatan

2015-10-01

Results from direct detection experiments are typically interpreted by employing an assumption about the dark matter velocity distribution, with results presented in the m{sub χ}−σ{sub n} plane. Recently methods which are independent of the DM halo velocity distribution have been developed which present results in the v{sub min}− g-tilde plane, but these in turn require an assumption on the dark matter mass. Here we present an extension of these halo-independent methods for dark matter direct detection which does not require a fiducial choice of the dark matter mass. With a change of variables from v{sub min} to nuclear recoil momentummore » (p{sub R}), the full halo-independent content of an experimental result for any dark matter mass can be condensed into a single plot as a function of a new halo integral variable, which we call h-tilde (p{sub R}). The entire family of conventional halo-independent g-tilde (v{sub min}) plots for all DM masses are directly found from the single h-tilde (p{sub R}) plot through a simple rescaling of axes. By considering results in h-tilde (p{sub R}) space, one can determine if two experiments are inconsistent for all masses and all physically possible halos, or for what range of dark matter masses the results are inconsistent for all halos, without the necessity of multiple g-tilde (v{sub min}) plots for different DM masses. We conduct a sample analysis comparing the CDMS II Si events to the null results from LUX, XENON10, and SuperCDMS using our method and discuss how the results can be strengthened by imposing the physically reasonable requirement of a finite halo escape velocity.« less

Halo-independent direct detection analyses without mass assumptions

DOE PAGES

Anderson, Adam J.; Fox, Patrick J.; Kahn, Yonatan; ...

2015-10-06

Results from direct detection experiments are typically interpreted by employing an assumption about the dark matter velocity distribution, with results presented in the m χ – σ n plane. Recently methods which are independent of the DM halo velocity distribution have been developed which present results in the v min – g ~ plane, but these in turn require an assumption on the dark matter mass. Here we present an extension of these halo-independent methods for dark matter direct detection which does not require a fiducial choice of the dark matter mass. With a change of variables from v minmore » to nuclear recoil momentum (p R), the full halo-independent content of an experimental result for any dark matter mass can be condensed into a single plot as a function of a new halo integral variable, which we call tilde h(p R). The entire family of conventional halo-independent tilde g ~(v min) plots for all DM masses are directly found from the single tilde h ~(p R) plot through a simple rescaling of axes. By considering results in tildeh ~(p R) space, one can determine if two experiments are inconsistent for all masses and all physically possible halos, or for what range of dark matter masses the results are inconsistent for all halos, without the necessity of multiple tilde g ~(v min) plots for different DM masses. As a result, we conduct a sample analysis comparing the CDMS II Si events to the null results from LUX, XENON10, and SuperCDMS using our method and discuss how the results can be strengthened by imposing the physically reasonable requirement of a finite halo escape velocity.« less

Comparative genome analysis of Pseudomonas genomes including Populus-associated isolates

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

Jun, Se Ran; Wassenaar, Trudy; Nookaew, Intawat

The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches including the rhizosphere and endosphere of many plants influencing phylogenetic diversity and heterogeneity. In this study, comparative genome analysis was performed on over one thousand Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides. Based on average amino acid identity, genomic clusters were identified within the Pseudomonas genus, which showed agreements with clades by NCBI and cliques by IMG. The P. fluorescens group was organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. The speciesmore » P. aeruginosa showed clear distinction in their genomic relatedness compared to other Pseudomonas species groups based on the pan and core genome analysis. The 19 isolates of our 21 Populus-associated isolates formed three distinct subgroups within the P. fluorescens major group, supported by pathway profiles analysis, while two isolates were more closely related to P. chlororaphis and P. putida. The specific genes to Populus-associated subgroups were identified where genes specific to subgroup 1 include several sensory systems such as proteins which act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor; specific genes to subgroup 2 contain unique hypothetical genes; and genes specific to subgroup 3 organisms have a different hydrolase activity. IMPORTANCE The comparative genome analyses of the genus Pseudomonas that included Populus-associated isolates resulted in novel insights into high diversity of Pseudomonas. Consistent and robust genomic clusters with phylogenetic homogeneity were identified, which resolved species-clades that are not clearly defined by 16S rRNA gene sequence analysis alone. The genomic clusters may be reflective of distinct ecological niches to which the organisms have adapted, but

Comparative genome analysis of Pseudomonas genomes including Populus-associated isolates

DOE PAGES

Jun, Se Ran; Wassenaar, Trudy; Nookaew, Intawat; ...

2016-01-01

The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches including the rhizosphere and endosphere of many plants influencing phylogenetic diversity and heterogeneity. In this study, comparative genome analysis was performed on over one thousand Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides. Based on average amino acid identity, genomic clusters were identified within the Pseudomonas genus, which showed agreements with clades by NCBI and cliques by IMG. The P. fluorescens group was organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. The speciesmore » P. aeruginosa showed clear distinction in their genomic relatedness compared to other Pseudomonas species groups based on the pan and core genome analysis. The 19 isolates of our 21 Populus-associated isolates formed three distinct subgroups within the P. fluorescens major group, supported by pathway profiles analysis, while two isolates were more closely related to P. chlororaphis and P. putida. The specific genes to Populus-associated subgroups were identified where genes specific to subgroup 1 include several sensory systems such as proteins which act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor; specific genes to subgroup 2 contain unique hypothetical genes; and genes specific to subgroup 3 organisms have a different hydrolase activity. IMPORTANCE The comparative genome analyses of the genus Pseudomonas that included Populus-associated isolates resulted in novel insights into high diversity of Pseudomonas. Consistent and robust genomic clusters with phylogenetic homogeneity were identified, which resolved species-clades that are not clearly defined by 16S rRNA gene sequence analysis alone. The genomic clusters may be reflective of distinct ecological niches to which the organisms have adapted, but

Comparing Mycobacterium tuberculosis genomes using genome topology networks.

PubMed

Jiang, Jianping; Gu, Jianlei; Zhang, Liang; Zhang, Chenyi; Deng, Xiao; Dou, Tonghai; Zhao, Guoping; Zhou, Yan

2015-02-14

Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. In this work, we introduce a 'Genome Topology Network' (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of 'unfixed ortholog' has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/ , and allows re-annotating the 'lost' genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

PubMed Central

Fong, Christine; Rohmer, Laurence; Radey, Matthew; Wasnick, Michael; Brittnacher, Mitchell J

2008-01-01

Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT) is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any web browser with no client

Comparative analysis and visualization of multiple collinear genomes

PubMed Central

2012-01-01

Background Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited to perform meaningful comparative analysis among a large number of genomes. With the increasing quantity and availability of genomic data, there is an increased burden to provide useful visualization and analysis tools for comparison of multiple collinear genomes such as the large panels of model organisms which are the basis for much of the current genetic research. Results We have developed a novel web-based tool for visualizing and analyzing multiple collinear genomes. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations. Conclusions Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse laboratory strains. PMID:22536897

Reference-free comparative genomics of 174 chloroplasts.

PubMed

Kua, Chai-Shian; Ruan, Jue; Harting, John; Ye, Cheng-Xi; Helmus, Matthew R; Yu, Jun; Cannon, Charles H

2012-01-01

Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across genomes [1]. We then assemble de novo contigs centered on informative variation. The localized de novo contigs can be separated into two major classes: tip = unique to a single genome and group = shared by a subset of genomes. Prior to assembly, we found that ~18% of the chloroplast was duplicated in the inverted repeat (IR) region across a four-fold difference in genome sizes, from a highly reduced parasitic orchid [2] to a massive algal chloroplast [3], including gnetophytes [4] and cycads [5]. The conservation of this ratio between single copy and duplicated sequence was basal among green plants, independent of photosynthesis and mechanism of genome size change, and different in gymnosperms and lower plants. Major lineages in the angiosperm clade differed in the pattern of shared kmers and de novo contigs. For example, parasitic plants demonstrated an expected accelerated overall rate of evolution, while the hemi-parasitic genomes contained a great deal more novel sequence than holo-parasitic plants, suggesting different mechanisms at different stages of genomic contraction. Additionally, the legumes are diverging more quickly and in different ways than other major families. Small duplicated fragments of the rrn23 genes were deeply conserved among seed plants, including among several species without the IR regions, indicating a crucial functional role of this duplication. Localized de novo assembly of informative kmers greatly reduces the complexity of large comparative analyses by confining the analysis to a small partition of data and genomes relevant to the specific question, allowing direct analysis of next-gen sequence data from previously unstudied genomes and

Mosaic Graphs and Comparative Genomics in Phage Communities

PubMed Central

Belcaid, Mahdi; Bergeron, Anne

2010-01-01

Abstract Comparing the genomes of two closely related viruses often produces mosaics where nearly identical sequences alternate with sequences that are unique to each genome. When several closely related genomes are compared, the unique sequences are likely to be shared with third genomes, leading to virus mosaic communities. Here we present comparative analysis of sets of Staphylococcus aureus phages that share large identical sequences with up to three other genomes, and with different partners along their genomes. We introduce mosaic graphs to represent these complex recombination events, and use them to illustrate the breath and depth of sequence sharing: some genomes are almost completely made up of shared sequences, while genomes that share very large identical sequences can adopt alternate functional modules. Mosaic graphs also allow us to identify breakpoints that could eventually be used for the construction of recombination networks. These findings have several implications on phage metagenomics assembly, on the horizontal gene transfer paradigm, and more generally on the understanding of the composition and evolutionary dynamics of virus communities. PMID:20874413

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

PubMed

Machado, Henrique; Gram, Lone

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

The halo current in ASDEX Upgrade

NASA Astrophysics Data System (ADS)

Pautasso, G.; Giannone, L.; Gruber, O.; Herrmann, A.; Maraschek, M.; Schuhbeck, K. H.; ASDEX Upgrade Team

2011-04-01

Due to the complexity of the phenomena involved, a self-consistent physical model for the prediction of the halo current is not available. Therefore the ITER specifications of the spatial distribution and evolution of the halo current rely on empirical assumptions. This paper presents the results of an extensive analysis of the halo current measured in ASDEX Upgrade with particular emphasis on the evolution of the halo region, on the magnitude and time history of the halo current, and on the structure and duration of its toroidal and poloidal asymmetries. The effective length of the poloidal path of the halo current in the vessel is found to be rather insensitive to plasma parameters. Large values of the toroidally averaged halo current are observed in both vertical displacement events and centred disruptions but last a small fraction of the current quench; they coincide typically with a large but short-lived MHD event.

The 6dF Galaxy Survey: dependence of halo occupation on stellar mass

NASA Astrophysics Data System (ADS)

Beutler, Florian; Blake, Chris; Colless, Matthew; Jones, D. Heath; Staveley-Smith, Lister; Campbell, Lachlan; Parker, Quentin; Saunders, Will; Watson, Fred

2013-03-01

In this paper we study the stellar mass dependence of galaxy clustering in the 6dF Galaxy Survey (6dFGS). The near-infrared selection of 6dFGS allows more reliable stellar mass estimates compared to optical bands used in other galaxy surveys. Using the halo occupation distribution model, we investigate the trend of dark matter halo mass and satellite fraction with stellar mass by measuring the projected correlation function, wp(rp). We find that the typical halo mass (M1) as well as the satellite power-law index (α) increases with stellar mass. This indicates (1) that galaxies with higher stellar mass sit in more massive dark matter haloes and (2) that these more massive dark matter haloes accumulate satellites faster with growing mass compared to haloes occupied by low stellar mass galaxies. Furthermore, we find a relation between M1 and the minimum dark matter halo mass (Mmin) of M1 ≈ 22 Mmin, in agreement with similar findings for Sloan Digital Sky Survey galaxies. The satellite fraction of 6dFGS galaxies declines with increasing stellar mass from 21 per cent at Mstellar = 2.6 × 1010 h-2 M⊙ to 12 per cent at Mstellar = 5.4 × 1010 h-2 M⊙ indicating that high stellar mass galaxies are more likely to be central galaxies. We compare our results to two different semi-analytic models derived from the Millennium Simulation, finding some disagreement. Our results can be used for placing new constraints on semi-analytic models in the future, particularly the behaviour of luminous red satellites. Finally, we compare our results to studies of halo occupation using galaxy-galaxy weak lensing. We find good overall agreement, representing a valuable cross-check for these two different tools of studying the matter distribution in the Universe.

Co-formation of the disc and the stellar halo

NASA Astrophysics Data System (ADS)

Belokurov, V.; Erkal, D.; Evans, N. W.; Koposov, S. E.; Deason, A. J.

2018-07-01

Using a large sample of main sequence stars with 7D measurements supplied by Gaia and SDSS, we study the kinematic properties of the local (within ˜10 kpc from the Sun) stellar halo. We demonstrate that the halo's velocity ellipsoid evolves strongly with metallicity. At the low-[Fe/H] end, the orbital anisotropy (the amount of motion in the radial direction compared with the tangential one) is mildly radial, with 0.2 <β< 0.4. For stars with [Fe/H] > -1.7, however, we measure extreme values of β˜ 0.9. Across the metallicity range considered, namely-3 < [Fe/H] < -1, the stellar halo's spin is minimal, at the level of 20< \\bar{v}_{θ }(kms^{-1}) < 30. Using a suite of cosmological zoom-in simulations of halo formation, we deduce that the observed acute anisotropy is inconsistent with the continuous accretion of dwarf satellites. Instead, we argue, the stellar debris in the inner halo was deposited in a major accretion event by a satellite with Mvir > 1010M⊙ around the epoch of the Galactic disc formation, between 8 and 11 Gyr ago. The radical halo anisotropy is the result of the dramatic radialization of the massive progenitor's orbit, amplified by the action of the growing disc.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

PubMed Central

Machado, Henrique; Gram, Lone

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms. PMID:28706512

Dependence of Halo Bias and Kinematics on Assembly Variables

NASA Astrophysics Data System (ADS)

Xu, Xiaoju; Zheng, Zheng

2018-06-01

Using dark matter haloes identified in a large N-body simulation, we study halo assembly bias, with halo formation time, peak maximum circular velocity, concentration, and spin as the assembly variables. Instead of grouping haloes at fixed mass into different percentiles of each assembly variable, we present the joint dependence of halo bias on the values of halo mass and each assembly variable. In the plane of halo mass and one assembly variable, the joint dependence can be largely described as halo bias increasing outward from a global minimum. We find it unlikely to have a combination of halo variables to absorb all assembly bias effects. We then present the joint dependence of halo bias on two assembly variables at fixed halo mass. The gradient of halo bias does not necessarily follow the correlation direction of the two assembly variables and it varies with halo mass. Therefore in general for two correlated assembly variables one cannot be used as a proxy for the other in predicting halo assembly bias trend. Finally, halo assembly is found to affect the kinematics of haloes. Low-mass haloes formed earlier can have much higher pairwise velocity dispersion than those of massive haloes. In general, halo assembly leads to a correlation between halo bias and halo pairwise velocity distribution, with more strongly clustered haloes having higher pairwise velocity and velocity dispersion. However, the correlation is not tight, and the kinematics of haloes at fixed halo bias still depends on halo mass and assembly variables.

Baryonic impact on the dark matter orbital properties of Milky Way-sized haloes

NASA Astrophysics Data System (ADS)

Zhu, Qirong; Hernquist, Lars; Marinacci, Federico; Springel, Volker; Li, Yuexing

2017-04-01

We study the orbital properties of dark matter haloes by combining a spectral method and cosmological simulations of Milky Way-sized Galaxies. We compare the dynamics and orbits of individual dark matter particles from both hydrodynamic and N-body simulations, and find that the fraction of box, tube and resonant orbits of the dark matter halo decreases significantly due to the effects of baryons. In particular, the central region of the dark matter halo in the hydrodynamic simulation is dominated by regular, short-axis tube orbits, in contrast to the chaotic, box and thin orbits dominant in the N-body run. This leads to a more spherical dark matter halo in the hydrodynamic run compared to a prolate one as commonly seen in the N-body simulations. Furthermore, by using a kernel-based density estimator, we compare the coarse-grained phase-space densities of dark matter haloes in both simulations and find that it is lower by ˜0.5 dex in the hydrodynamic run due to changes in the angular momentum distribution, which indicates that the baryonic process that affects the dark matter is irreversible. Our results imply that baryons play an important role in determining the shape, kinematics and phase-space density of dark matter haloes in galaxies.

The E3 Ubiquitin Ligase MIB-1 Is Necessary To Form the Nuclear Halo in Caenorhabditis elegans Sperm.

PubMed

Herrera, Leslie A; Starr, Daniel A

2018-05-18

Unlike the classical nuclear envelope with two membranes found in other eukaryotic cells, most nematode sperm nuclei are not encapsulated by membranes. Instead, they are surrounded by a nuclear halo of unknown composition. How the halo is formed and regulated is unknown. We used forward genetics to identify molecular lesions behind three classical fer (fertilization defective) mutations that disrupt the ultrastructure of the Caenorhabditis elegans sperm nuclear halo. We found fer-2 and fer-4 alleles to be nonsense mutations in mib-1. fer-3 was caused by a nonsense mutation in eri-3 GFP::MIB-1 was expressed in the germline during early spermatogenesis, but not in mature sperm. mib-1 encodes a conserved E3 ubiquitin ligase homologous to vertebrate Mib1 and Mib2, which function in Notch signaling. Here, we show that mib-1 is important for male sterility and is involved in the regulation or formation of the nuclear halo during nematode spermatogenesis. Copyright © 2018, G3: Genes, Genomes, Genetics.

Comparison of two laboratory-based systems for evaluation of halos in intraocular lenses

PubMed Central

Alexander, Elsinore; Wei, Xin; Lee, Shinwook

2018-01-01

Purpose Multifocal intraocular lenses (IOLs) can be associated with unwanted visual phenomena, including halos. Predicting potential for halos is desirable when designing new multifocal IOLs. Halo images from 6 IOL models were compared using the Optikos modulation transfer function bench system and a new high dynamic range (HDR) system. Materials and methods One monofocal, 1 extended depth of focus, and 4 multifocal IOLs were evaluated. An off-the-shelf optical bench was used to simulate a distant (>50 m) car headlight and record images. A custom HDR system was constructed using an imaging photometer to simulate headlight images and to measure quantitative halo luminance data. A metric was developed to characterize halo luminance properties. Clinical relevance was investigated by correlating halo measurements to visual outcomes questionnaire data. Results The Optikos system produced halo images useful for visual comparisons; however, measurements were relative and not quantitative. The HDR halo system provided objective and quantitative measurements used to create a metric from the area under the curve (AUC) of the logarithmic normalized halo profile. This proposed metric differentiated between IOL models, and linear regression analysis found strong correlations between AUC and subjective clinical ratings of halos. Conclusion The HDR system produced quantitative, preclinical metrics that correlated to patients’ subjective perception of halos. PMID:29503526

Gramene 2013: Comparative plant genomics resources

USDA-ARS?s Scientific Manuscript database

Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework fo...

Dynamical Constraints On The Galaxy-Halo Connection

NASA Astrophysics Data System (ADS)

Desmond, Harry

2017-07-01

Dark matter halos comprise the bulk of the universe's mass, yet must be probed by the luminous galaxies that form within them. A key goal of modern astrophysics, therefore, is to robustly relate the visible and dark mass, which to first order means relating the properties of galaxies and halos. This may be expected not only to improve our knowledge of galaxy formation, but also to enable high-precision cosmological tests using galaxies and hence maximise the utility of future galaxy surveys. As halos are inaccessible to observations - as galaxies are to N-body simulations - this relation requires an additional modelling step.The aim of this thesis is to develop and evaluate models of the galaxy-halo connection using observations of galaxy dynamics. In particular, I build empirical models based on the technique of halo abundance matching for five key dynamical scaling relations of galaxies - the Tully-Fisher, Faber-Jackson, mass-size and mass discrepancy-acceleration relations, and Fundamental Plane - which relate their baryon distributions and rotation or velocity dispersion profiles. I then develop a statistical scheme based on approximate Bayesian computation to compare the predicted and measured values of a number of summary statistics describing the relations' important features. This not only provides quantitative constraints on the free parameters of the models, but also allows absolute goodness-of-fit measures to be formulated. I find some features to be naturally accounted for by an abundance matching approach and others to impose new constraints on the galaxy-halo connection; the remainder are challenging to account for and may imply galaxy-halo correlations beyond the scope of basic abundance matching.Besides providing concrete statistical tests of specific galaxy formation theories, these results will be of use for guiding the inputs of empirical and semi-analytic galaxy formation models, which require galaxy-halo correlations to be imposed by hand. As

SPHERES HALO

NASA Image and Video Library

2017-06-23

iss052e006482 (6/23/2017) --- Astronaut Peggy Whitson is photographed during a test session of the Synchronized Position Hold, Engage, Reorient, Experimental Satellites (SPHERES) Halo investigation in the Kibo module. The SPHERES Halo investigation studies the possibility of launching several separate components and then attaching them once they are in space. The investigation upgrades the International Space Station’s fleet of SPHERES to enable each SPHERE to communicate with six external objects at the same time, testing new control and remote assembly methods.

The Anemic Stellar Halo of M101

NASA Astrophysics Data System (ADS)

Holwerda, Benne

2014-10-01

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

Reference-Free Comparative Genomics of 174 Chloroplasts

PubMed Central

Kua, Chai-Shian; Ruan, Jue; Harting, John; Ye, Cheng-Xi; Helmus, Matthew R.; Yu, Jun; Cannon, Charles H.

2012-01-01

Direct analysis of unassembled genomic data could greatly increase the power of short read DNA sequencing technologies and allow comparative genomics of organisms without a completed reference available. Here, we compare 174 chloroplasts by analyzing the taxanomic distribution of short kmers across genomes [1]. We then assemble de novo contigs centered on informative variation. The localized de novo contigs can be separated into two major classes: tip = unique to a single genome and group = shared by a subset of genomes. Prior to assembly, we found that ∼18% of the chloroplast was duplicated in the inverted repeat (IR) region across a four-fold difference in genome sizes, from a highly reduced parasitic orchid [2] to a massive algal chloroplast [3], including gnetophytes [4] and cycads [5]. The conservation of this ratio between single copy and duplicated sequence was basal among green plants, independent of photosynthesis and mechanism of genome size change, and different in gymnosperms and lower plants. Major lineages in the angiosperm clade differed in the pattern of shared kmers and de novo contigs. For example, parasitic plants demonstrated an expected accelerated overall rate of evolution, while the hemi-parasitic genomes contained a great deal more novel sequence than holo-parasitic plants, suggesting different mechanisms at different stages of genomic contraction. Additionally, the legumes are diverging more quickly and in different ways than other major families. Small duplicated fragments of the rrn23 genes were deeply conserved among seed plants, including among several species without the IR regions, indicating a crucial functional role of this duplication. Localized de novo assembly of informative kmers greatly reduces the complexity of large comparative analyses by confining the analysis to a small partition of data and genomes relevant to the specific question, allowing direct analysis of next-gen sequence data from previously unstudied

Large-scale assembly bias of dark matter halos

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

Lazeyras, Titouan; Musso, Marcello; Schmidt, Fabian, E-mail: titouan@mpa-garching.mpg.de, E-mail: mmusso@sas.upenn.edu, E-mail: fabians@mpa-garching.mpg.de

We present precise measurements of the assembly bias of dark matter halos, i.e. the dependence of halo bias on other properties than the mass, using curved 'separate universe' N-body simulations which effectively incorporate an infinite-wavelength matter overdensity into the background density. This method measures the LIMD (local-in-matter-density) bias parameters b {sub n} in the large-scale limit. We focus on the dependence of the first two Eulerian biases b {sup E} {sup {sub 1}} and b {sup E} {sup {sub 2}} on four halo properties: the concentration, spin, mass accretion rate, and ellipticity. We quantitatively compare our results with previous worksmore » in which assembly bias was measured on fairly small scales. Despite this difference, our findings are in good agreement with previous results. We also look at the joint dependence of bias on two halo properties in addition to the mass. Finally, using the excursion set peaks model, we attempt to shed new insights on how assembly bias arises in this analytical model.« less

Observing halos through airplane windows

NASA Astrophysics Data System (ADS)

Shaw, Joseph A.

2017-09-01

A halo is one of the most frequent and impressive optical phenomena easily observable in the sky. It is also one of the natural optical phenomena most often visible through an airplane window. Halos and related phenomena vary from a single spot of light formed by reflection of the sun from the tops of plate-shaped ice crystals to large rings with splashes of colors, caused by a combination of reflection and refraction in ice crystals. Even with extreme heat at the ground, an airplane quickly rises through sufficient altitude to find ice crystals in the clouds, enabling an alert passenger (or pilot) to see ice-crystal optical phenomena. This paper briefly reviews these phenomena with photographs and diagrams. Photographs include commonly seen halos, as well as Bottlinger's rings, a rare halo that is still not fully explained. Tips are given for enhancing your chances of seeing and understanding halos.

Halo-free Phase Contrast Microscopy

NASA Astrophysics Data System (ADS)

Nguyen, Tan H.; Kandel, Mikhail; Shakir, Haadi M.; Best-Popescu, Catherine; Arikkath, Jyothi; Do, Minh N.; Popescu, Gabriel

2017-03-01

We present a new approach for retrieving halo-free phase contrast microscopy (hfPC) images by upgrading the conventional PC microscope with an external interferometric module, which generates sufficient data for reversing the halo artifact. Acquiring four independent intensity images, our approach first measures haloed phase maps of the sample. We solve for the halo-free sample transmission function by using a physical model of the image formation under partial spatial coherence. Using this halo-free sample transmission, we can numerically generate artifact-free PC images. Furthermore, this transmission can be further used to obtain quantitative information about the sample, e.g., the thickness with known refractive indices, dry mass of live cells during their cycles. We tested our hfPC method on various control samples, e.g., beads, pillars and validated its potential for biological investigation by imaging live HeLa cells, red blood cells, and neurons.

Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement.

PubMed

Butler, J B; Vaillancourt, R E; Potts, B M; Lee, D J; King, G J; Baten, A; Shepherd, M; Freeman, J S

2017-05-22

Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes. We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps. These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.

DCODE.ORG Anthology of Comparative Genomic Tools

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

Loots, G G; Ovcharenko, I

2005-01-11

Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the noncoding encryption of gene regulation across genomes. To facilitate the use of comparative genomics to practical applications in genetics and genomics we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools: zPicture and Mulan; a phylogenetic shadowing tool: eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools: rVista and multiTF; a toolmore » for extracting cis-regulatory modules governing the expression of co-regulated genes, CREME; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ web site.« less

Halo modelling in chameleon theories

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

Lombriser, Lucas; Koyama, Kazuya; Li, Baojiu, E-mail: lucas.lombriser@port.ac.uk, E-mail: kazuya.koyama@port.ac.uk, E-mail: baojiu.li@durham.ac.uk

2014-03-01

We analyse modelling techniques for the large-scale structure formed in scalar-tensor theories of constant Brans-Dicke parameter which match the concordance model background expansion history and produce a chameleon suppression of the gravitational modification in high-density regions. Thereby, we use a mass and environment dependent chameleon spherical collapse model, the Sheth-Tormen halo mass function and linear halo bias, the Navarro-Frenk-White halo density profile, and the halo model. Furthermore, using the spherical collapse model, we extrapolate a chameleon mass-concentration scaling relation from a ΛCDM prescription calibrated to N-body simulations. We also provide constraints on the model parameters to ensure viability on localmore » scales. We test our description of the halo mass function and nonlinear matter power spectrum against the respective observables extracted from large-volume and high-resolution N-body simulations in the limiting case of f(R) gravity, corresponding to a vanishing Brans-Dicke parameter. We find good agreement between the two; the halo model provides a good qualitative description of the shape of the relative enhancement of the f(R) matter power spectrum with respect to ΛCDM caused by the extra attractive gravitational force but fails to recover the correct amplitude. Introducing an effective linear power spectrum in the computation of the two-halo term to account for an underestimation of the chameleon suppression at intermediate scales in our approach, we accurately reproduce the measurements from the N-body simulations.« less

Comparative analysis of prophages in Streptococcus mutans genomes

PubMed Central

Fu, Tiwei; Fan, Xiangyu; Long, Quanxin; Deng, Wanyan; Song, Jinlin

2017-01-01

Prophages have been considered genetic units that have an intimate association with novel phenotypic properties of bacterial hosts, such as pathogenicity and genomic variation. Little is known about the genetic information of prophages in the genome of Streptococcus mutans, a major pathogen of human dental caries. In this study, we identified 35 prophage-like elements in S. mutans genomes and performed a comparative genomic analysis. Comparative genomic and phylogenetic analyses of prophage sequences revealed that the prophages could be classified into three main large clusters: Cluster A, Cluster B, and Cluster C. The S. mutans prophages in each cluster were compared. The genomic sequences of phismuN66-1, phismuNLML9-1, and phismu24-1 all shared similarities with the previously reported S. mutans phages M102, M102AD, and ϕAPCM01. The genomes were organized into seven major gene clusters according to the putative functions of the predicted open reading frames: packaging and structural modules, integrase, host lysis modules, DNA replication/recombination modules, transcriptional regulatory modules, other protein modules, and hypothetical protein modules. Moreover, an integrase gene was only identified in phismuNLML9-1 prophages. PMID:29158986

Genome-Wide Linkage and Association Mapping of Halo Blight Resistance in Common Bean to Race 6 of the Globally Important Bacterial Pathogen

PubMed Central

Tock, Andrew J.; Fourie, Deidré; Walley, Peter G.; Holub, Eric B.; Soler, Alvaro; Cichy, Karen A.; Pastor-Corrales, Marcial A.; Song, Qijian; Porch, Timothy G.; Hart, John P.; Vasconcellos, Renato C. C.; Vicente, Joana G.; Barker, Guy C.; Miklas, Phillip N.

2017-01-01

Pseudomonas syringae pv. phaseolicola (Psph) Race 6 is a globally prevalent and broadly virulent bacterial pathogen with devastating impact causing halo blight of common bean (Phaseolus vulgaris L.). Common bean lines PI 150414 and CAL 143 are known sources of resistance against this pathogen. We constructed high-resolution linkage maps for three recombinant inbred populations to map resistance to Psph Race 6 derived from the two common bean lines. This was complemented with a genome-wide association study (GWAS) of Race 6 resistance in an Andean Diversity Panel of common bean. Race 6 resistance from PI 150414 maps to a single major-effect quantitative trait locus (QTL; HB4.2) on chromosome Pv04 and confers broad-spectrum resistance to eight other races of the pathogen. Resistance segregating in a Rojo × CAL 143 population maps to five chromosome arms and includes HB4.2. GWAS detected one QTL (HB5.1) on chromosome Pv05 for resistance to Race 6 with significant influence on seed yield. The same HB5.1 QTL, found in both Canadian Wonder × PI 150414 and Rojo × CAL 143 populations, was effective against Race 6 but lacks broad resistance. This study provides evidence for marker-assisted breeding for more durable halo blight control in common bean by combining alleles of race-nonspecific resistance (HB4.2 from PI 150414) and race-specific resistance (HB5.1 from cv. Rojo). PMID:28736566

Improving fast generation of halo catalogues with higher order Lagrangian perturbation theory

NASA Astrophysics Data System (ADS)

Munari, Emiliano; Monaco, Pierluigi; Sefusatti, Emiliano; Castorina, Emanuele; Mohammad, Faizan G.; Anselmi, Stefano; Borgani, Stefano

2017-03-01

We present the latest version of PINOCCHIO, a code that generates catalogues of dark matter haloes in an approximate but fast way with respect to an N-body simulation. This code version implements a new on-the-fly production of halo catalogue on the past light cone with continuous time sampling, and the computation of particle and halo displacements are extended up to third-order Lagrangian perturbation theory (LPT), in contrast with previous versions that used Zel'dovich approximation. We run PINOCCHIO on the same initial configuration of a reference N-body simulation, so that the comparison extends to the object-by-object level. We consider haloes at redshifts 0 and 1, using different LPT orders either for halo construction or to compute halo final positions. We compare the clustering properties of PINOCCHIO haloes with those from the simulation by computing the power spectrum and two-point correlation function in real and redshift space (monopole and quadrupole), the bispectrum and the phase difference of halo distributions. We find that 2LPT and 3LPT give noticeable improvement. 3LPT provides the best agreement with N-body when it is used to displace haloes, while 2LPT gives better results for constructing haloes. At the highest orders, linear bias is typically recovered at a few per cent level. In Fourier space and using 3LPT for halo displacements, the halo power spectrum is recovered to within 10 per cent up to kmax ∼ 0.5 h Mpc-1. The results presented in this paper have interesting implications for the generation of large ensemble of mock surveys for the scientific exploitation of data from big surveys.

Dcode.org anthology of comparative genomic tools.

PubMed

Loots, Gabriela G; Ovcharenko, Ivan

2005-07-01

Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the non-coding encryption of gene regulation across genomes. To facilitate the practical application of comparative sequence analysis to genetics and genomics, we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools, zPicture and Mulan; a phylogenetic shadowing tool, eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools, rVista and multiTF; a tool for extracting cis-regulatory modules governing the expression of co-regulated genes, Creme 2.0; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here, we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ website.

Analytical halo model of galactic conformity

NASA Astrophysics Data System (ADS)

Pahwa, Isha; Paranjape, Aseem

2017-09-01

We present a fully analytical halo model of colour-dependent clustering that incorporates the effects of galactic conformity in a halo occupation distribution framework. The model, based on our previous numerical work, describes conformity through a correlation between the colour of a galaxy and the concentration of its parent halo, leading to a correlation between central and satellite galaxy colours at fixed halo mass. The strength of the correlation is set by a tunable 'group quenching efficiency', and the model can separately describe group-level correlations between galaxy colour (1-halo conformity) and large-scale correlations induced by assembly bias (2-halo conformity). We validate our analytical results using clustering measurements in mock galaxy catalogues, finding that the model is accurate at the 10-20 per cent level for a wide range of luminosities and length-scales. We apply the formalism to interpret the colour-dependent clustering of galaxies in the Sloan Digital Sky Survey (SDSS). We find good overall agreement between the data and a model that has 1-halo conformity at a level consistent with previous results based on an SDSS group catalogue, although the clustering data require satellites to be redder than suggested by the group catalogue. Within our modelling uncertainties, however, we do not find strong evidence of 2-halo conformity driven by assembly bias in SDSS clustering.

The Spin and Orientation of Dark Matter Halos Within Cosmic Filaments

NASA Astrophysics Data System (ADS)

Zhang, Youcai; Yang, Xiaohu; Faltenbacher, Andreas; Springel, Volker; Lin, Weipeng; Wang, Huiyuan

2009-11-01

Clusters, filaments, sheets, and voids are the building blocks of the cosmic web. Forming dark matter halos respond to these different large-scale environments, and this in turn affects the properties of galaxies hosted by the halos. It is therefore important to understand the systematic correlations of halo properties with the morphology of the cosmic web, as this informs both about galaxy formation physics and possible systematics of weak lensing studies. In this study, we present and compare two distinct algorithms for finding cosmic filaments and sheets, a task which is far less well established than the identification of dark matter halos or voids. One method is based on the smoothed dark matter density field and the other uses the halo distributions directly. We apply both techniques to one high-resolution N-body simulation and reconstruct the filamentary/sheet like network of the dark matter density field. We focus on investigating the properties of the dark matter halos inside these structures, in particular, on the directions of their spins and the orientation of their shapes with respect to the directions of the filaments and sheets. We find that both the spin and the major axes of filament halos with masses lsim1013 h -1 M sun are preferentially aligned with the direction of the filaments. The spins and major axes of halos in sheets tend to lie parallel to the sheets. There is an opposite mass dependence of the alignment strength for the spin (negative) and major (positive) axes, i.e. with increasing halo mass the major axis tends to be more strongly aligned with the direction of the filament, whereas the alignment between halo spin and filament becomes weaker with increasing halo mass. The alignment strength as a function of the distance to the most massive node halo indicates that there is a transit large-scale environment impact: from the two-dimensional collapse phase of the filament to the three-dimensional collapse phase of the cluster/node halo at

Sequencing and comparing whole mitochondrial genomes ofanimals

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

Boore, Jeffrey L.; Macey, J. Robert; Medina, Monica

2005-04-22

Comparing complete animal mitochondrial genome sequences is becoming increasingly common for phylogenetic reconstruction and as a model for genome evolution. Not only are they much more informative than shorter sequences of individual genes for inferring evolutionary relatedness, but these data also provide sets of genome-level characters, such as the relative arrangements of genes, that can be especially powerful. We describe here the protocols commonly used for physically isolating mtDNA, for amplifying these by PCR or RCA, for cloning,sequencing, assembly, validation, and gene annotation, and for comparing both sequences and gene arrangements. On several topics, we offer general observations based onmore » our experiences to date with determining and comparing complete mtDNA sequences.« less

Deep brain transcranial magnetic stimulation using variable "Halo coil" system

NASA Astrophysics Data System (ADS)

Meng, Y.; Hadimani, R. L.; Crowther, L. J.; Xu, Z.; Qu, J.; Jiles, D. C.

2015-05-01

Transcranial Magnetic Stimulation has the potential to treat various neurological disorders non-invasively and safely. The "Halo coil" configuration can stimulate deeper regions of the brain with lower surface to deep-brain field ratio compared to other coil configurations. The existing "Halo coil" configuration is fixed and is limited in varying the site of stimulation in the brain. We have developed a new system based on the current "Halo coil" design along with a graphical user interface system that enables the larger coil to rotate along the transverse plane. The new system can also enable vertical movement of larger coil. Thus, this adjustable "Halo coil" configuration can stimulate different regions of the brain by adjusting the position and orientation of the larger coil on the head. We have calculated magnetic and electric fields inside a MRI-derived heterogeneous head model for various positions and orientations of the coil. We have also investigated the mechanical and thermal stability of the adjustable "Halo coil" configuration for various positions and orientations of the coil to ensure safe operation of the system.

Taking Halo-Independent Dark Matter Methods Out of the Bin

DOE PAGES

Fox, Patrick J.; Kahn, Yonatan; McCullough, Matthew

2014-10-30

We develop a new halo-independent strategy for analyzing emerging DM hints, utilizing the method of extended maximum likelihood. This approach does not require the binning of events, making it uniquely suited to the analysis of emerging DM direct detection hints. It determines a preferred envelope, at a given confidence level, for the DM velocity integral which best fits the data using all available information and can be used even in the case of a single anomalous scattering event. All of the halo-independent information from a direct detection result may then be presented in a single plot, allowing simple comparisons betweenmore » multiple experiments. This results in the halo-independent analogue of the usual mass and cross-section plots found in typical direct detection analyses, where limit curves may be compared with best-fit regions in halo-space. The method is straightforward to implement, using already-established techniques, and its utility is demonstrated through the first unbinned halo-independent comparison of the three anomalous events observed in the CDMS-Si detector with recent limits from the LUX experiment.« less

The dog genome map and its use in mammalian comparative genomics.

PubMed

Switonski, Marek; Szczerbal, Izabela; Nowacka, Joanna

2004-01-01

The dog genome organization was extensively studied in the last ten years. The most important achievements are the well-developed marker genome maps, including over 3200 marker loci, and a survey of the DNA genome sequence. This knowledge, along with the most advanced map of the human genome, turned out to be very useful in comparative genomic studies. On the one hand, it has promoted the development of marker genome maps of other species of the family Canidae (red fox, arctic fox, Chinese raccoon dog) as well as studies on the evolution of their karyotype. But the most important approach is the comparative analysis of human and canine hereditary diseases. At present, causative gene mutations are known for 30 canine hereditary diseases. A majority of them have human counterparts with similar clinical and molecular features. Studies on identification of genes having a major impact on some multifactorial diseases (hip dysplasia, epilepsy) and cancers (multifocal renal cystadenocarcinoma and nodular dermatofibrosis) are advanced. Very promising are the results of gene therapy for certain canine monogenic diseases (haemophilia, hereditary retinal dystrophy, mucopolysaccharidosis), which have human equivalents. The above-mentioned examples prove a very important model role of the dog in studies of human genetic diseases. On the other hand, the identification of gene mutations responsible for hereditary diseases has a substantial impact on breeding strategy in the dog.

Jupiter Ring Halo

NASA Image and Video Library

1998-03-26

A mosaic of four images taken through the clear filter (610 nanometers) of the solid state imaging (CCD) system aboard NASA's Galileo spacecraft on November 8, 1996, at a resolution of approximately 46 kilometers (km) per picture element (pixel) along the rings; however, because the spacecraft was only about 0.5 degrees above the ring plane, the image is highly foreshortened in the vertical direction. The images were obtained when Galileo was in Jupiter's shadow peering back toward the Sun; the ring was approximately 2,300,000 kilometers (km) away. The arc on the far right of the image is produced by sunlight scattered by small particles comprising Jupiter's upper atmospheric haze. The ring also efficiently scatters light, indicating that much of its brightness is due to particles that are microns or less in diameter. Such small particles are believed to have human-scale lifetimes, i.e., very brief compared to the solar system's age. Jupiter's ring system is composed of three parts -- a flat main ring, a lenticular halo interior to the main ring, and the gossamer ring, which lies exterior to the main ring. The near and far arms of Jupiter's main ring extend horizontally across the mosaic, joining together at the ring's ansa, on the far left side of the figure. The near arm of the ring appears to be abruptly truncated close to the planet, at the point where it passes into Jupiter's shadow. A faint mist of particles can be seen above and below the main rings; this vertically extended, toroidal "halo" is unusual in planetary rings, and is probably caused by electromagnetic forces which can push small grains out of the ring plane. Halo material is present across this entire image, implying that it reaches more than 27,000 km above the ring plane. Because of shadowing, the halo is not visible close to Jupiter in the lower right part of the mosaic. In order to accentuate faint features in the image, different brightnesses are shown through color, with the brightest being

Probing the shape and internal structure of dark matter haloes with the halo-shear-shear three-point correlation function

NASA Astrophysics Data System (ADS)

Shirasaki, Masato; Yoshida, Naoki

2018-04-01

Weak lensing three-point statistics are powerful probes of the structure of dark matter haloes. We propose to use the correlation of the positions of galaxies with the shapes of background galaxy pairs, known as the halo-shear-shear correlation (HSSC), to measure the mean halo ellipticity and the abundance of subhaloes in a statistical manner. We run high-resolution cosmological N-body simulations and use the outputs to measure the HSSC for galaxy haloes and cluster haloes. Non-spherical haloes cause a characteristic azimuthal variation of the HSSC, and massive subhaloes in the outer region near the virial radius contribute to ˜ 10 per cent of the HSSC amplitude. Using the HSSC and its covariance estimated from our N-body simulations, we make forecast for constraining the internal structure of dark matter haloes with future galaxy surveys. With 1000 galaxy groups with mass greater than 1013.5 h-1M⊙, the average halo ellipticity can be measured with an accuracy of 10 percent. A spherical, smooth mass distribution can be ruled out at a ˜5σ significance level. The existence of subhaloes whose masses are in 1-10 percent of the main halo mass can be detected with ˜104 galaxies/clusters. We conclude that the HSSC provides valuable information on the structure of dark haloes and hence on the nature of dark matter.

IMGD: an integrated platform supporting comparative genomics and phylogenetics of insect mitochondrial genomes

PubMed Central

Lee, Wonhoon; Park, Jongsun; Choi, Jaeyoung; Jung, Kyongyong; Park, Bongsoo; Kim, Donghan; Lee, Jaeyoung; Ahn, Kyohun; Song, Wonho; Kang, Seogchan; Lee, Yong-Hwan; Lee, Seunghwan

2009-01-01

Background Sequences and organization of the mitochondrial genome have been used as markers to investigate evolutionary history and relationships in many taxonomic groups. The rapidly increasing mitochondrial genome sequences from diverse insects provide ample opportunities to explore various global evolutionary questions in the superclass Hexapoda. To adequately support such questions, it is imperative to establish an informatics platform that facilitates the retrieval and utilization of available mitochondrial genome sequence data. Results The Insect Mitochondrial Genome Database (IMGD) is a new integrated platform that archives the mitochondrial genome sequences from 25,747 hexapod species, including 112 completely sequenced and 20 nearly completed genomes and 113,985 partially sequenced mitochondrial genomes. The Species-driven User Interface (SUI) of IMGD supports data retrieval and diverse analyses at multi-taxon levels. The Phyloviewer implemented in IMGD provides three methods for drawing phylogenetic trees and displays the resulting trees on the web. The SNP database incorporated to IMGD presents the distribution of SNPs and INDELs in the mitochondrial genomes of multiple isolates within eight species. A newly developed comparative SNU Genome Browser supports the graphical presentation and interactive interface for the identified SNPs/INDELs. Conclusion The IMGD provides a solid foundation for the comparative mitochondrial genomics and phylogenetics of insects. All data and functions described here are available at the web site . PMID:19351385

THE SEGUE K GIANT SURVEY. III. QUANTIFYING GALACTIC HALO SUBSTRUCTURE

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

Janesh, William; Morrison, Heather L.; Ma, Zhibo

2016-01-10

We statistically quantify the amount of substructure in the Milky Way stellar halo using a sample of 4568 halo K giant stars at Galactocentric distances ranging over 5–125 kpc. These stars have been selected photometrically and confirmed spectroscopically as K giants from the Sloan Digital Sky Survey’s Sloan Extension for Galactic Understanding and Exploration project. Using a position–velocity clustering estimator (the 4distance) and a model of a smooth stellar halo, we quantify the amount of substructure in the halo, divided by distance and metallicity. Overall, we find that the halo as a whole is highly structured. We also confirm earliermore » work using blue horizontal branch (BHB) stars which showed that there is an increasing amount of substructure with increasing Galactocentric radius, and additionally find that the amount of substructure in the halo increases with increasing metallicity. Comparing to resampled BHB stars, we find that K giants and BHBs have similar amounts of substructure over equivalent ranges of Galactocentric radius. Using a friends-of-friends algorithm to identify members of individual groups, we find that a large fraction (∼33%) of grouped stars are associated with Sgr, and identify stars belonging to other halo star streams: the Orphan Stream, the Cetus Polar Stream, and others, including previously unknown substructures. A large fraction of sample K giants (more than 50%) are not grouped into any substructure. We find also that the Sgr stream strongly dominates groups in the outer halo for all except the most metal-poor stars, and suggest that this is the source of the increase of substructure with Galactocentric radius and metallicity.« less

Gramene database: navigating plant comparative genomics resources

USDA-ARS?s Scientific Manuscript database

Gramene (http://www.gramene.org) is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationship...

Charge radius of the 13N* proton halo nucleus with Halo Effective Field Theory

NASA Astrophysics Data System (ADS)

Mosavi Khansari, M.; Khalili, H.; Sadeghi, H.

2018-02-01

We evaluated the charge radius of the first excited state of 13N with halo Effective Field Theory (hEFT) at the low energies. The halo effective field theory without pion is used to examine the halo nucleus bound state with a large S-wave scattering length. We built Lagrangian from the effective core and the valence proton of the fields and obtained the charge form factor at Leading-Order (LO). The charge radius at leading order for the first excited state of the proton halo nucleus, 13N, has been estimated as rc = 2.52 fm. This result is without any finite-size contributions included from the core and the proton. If we consider the contributions of the charge radius of the proton and the core, the result will be [rC]13N* = 5.85 fm.

ULTRAVIOLET HALOS AROUND SPIRAL GALAXIES. I. MORPHOLOGY

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

Hodges-Kluck, Edmund; Cafmeyer, Julian; Bregman, Joel N., E-mail: hodgeskl@umich.edu

2016-12-10

We examine ultraviolet halos around a sample of highly inclined galaxies within 25 Mpc to measure their morphology and luminosity. Despite contamination from galactic light scattered into the wings of the point-spread function, we find that ultraviolet (UV) halos occur around each galaxy in our sample. Around most galaxies the halos form a thick, diffuse disk-like structure, but starburst galaxies with galactic superwinds have qualitatively different halos that are more extensive and have filamentary structure. The spatial coincidence of the UV halos above star-forming regions, the lack of consistent association with outflows or extraplanar ionized gas, and the strong correlationmore » between the halo and galaxy UV luminosity suggest that the UV light is an extragalactic reflection nebula. UV halos may thus represent 10{sup 6}–10{sup 7} M {sub ⊙} of dust within 2–10 kpc of the disk, whose properties may change with height in starburst galaxies.« less

Real- and redshift-space halo clustering in f(R) cosmologies

NASA Astrophysics Data System (ADS)

Arnalte-Mur, Pablo; Hellwing, Wojciech A.; Norberg, Peder

2017-05-01

We present two-point correlation function statistics of the mass and the haloes in the chameleon f(R) modified gravity scenario using a series of large-volume N-body simulations. Three distinct variations of f(R) are considered (F4, F5 and F6) and compared to a fiducial Λ cold dark matter (ΛCDM) model in the redshift range z ∈ [0, 1]. We find that the matter clustering is indistinguishable for all models except for F4, which shows a significantly steeper slope. The ratio of the redshift- to real-space correlation function at scales >20 h-1 Mpc agrees with the linear General Relativity (GR) Kaiser formula for the viable f(R) models considered. We consider three halo populations characterized by spatial abundances comparable to that of luminous red galaxies and galaxy clusters. The redshift-space halo correlation functions of F4 and F5 deviate significantly from ΛCDM at intermediate and high redshift, as the f(R) halo bias is smaller than or equal to that of the ΛCDM case. Finally, we introduce a new model-independent clustering statistic to distinguish f(R) from GR: the relative halo clustering ratio - R. The sampling required to adequately reduce the scatter in R will be available with the advent of the next-generation galaxy redshift surveys. This will foster a prospective avenue to obtain largely model-independent cosmological constraints on this class of modified gravity models.

Leveraging the rice genome sequence for monocot comparative and translational genomics.

PubMed

Lohithaswa, H C; Feltus, F A; Singh, H P; Bacon, C D; Bailey, C D; Paterson, A H

2007-07-01

Common genome anchor points across many taxa greatly facilitate translational and comparative genomics and will improve our understanding of the Tree of Life. To add to the repertoire of genomic tools applicable to the study of monocotyledonous plants in general, we aligned Allium and Musa ESTs to Oryza BAC sequences and identified candidate Allium-Oryza and Musa-Oryza conserved intron-scanning primers (CISPs). A random sampling of 96 CISP primer pairs, representing loci from 11 of the 12 chromosomes in rice, were tested on seven members of the order Poales and on representatives of the Arecales, Asparagales, and Zingiberales monocot orders. The single-copy amplification success rates of Allium (31.3%), Cynodon (31.4%), Hordeum (30.2%), Musa (37.5%), Oryza (61.5%), Pennisetum (33.3%), Sorghum (47.9%), Zea (33.3%), Triticum (30.2%), and representatives of the palm family (32.3%) suggest that subsets of these primers will provide DNA markers suitable for comparative and translational genomics in orphan crops, as well as for applications in conservation biology, ecology, invasion biology, population biology, systematic biology, and related fields.

THE DUAL ORIGIN OF STELLAR HALOS

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

Zolotov, Adi; Hogg, David W.; Willman, Beth

2009-09-10

We investigate the formation of the stellar halos of four simulated disk galaxies using high-resolution, cosmological SPH + N-body simulations. These simulations include a self-consistent treatment of all the major physical processes involved in galaxy formation. The simulated galaxies presented here each have a total mass of {approx}10{sup 12} M{sub sun}, but span a range of merger histories. These simulations allow us to study the competing importance of in situ star formation (stars formed in the primary galaxy) and accretion of stars from subhalos in the building of stellar halos in a {lambda}CDM universe. All four simulated galaxies are surroundedmore » by a stellar halo, whose inner regions (r < 20 kpc) contain both accreted stars, and an in situ stellar population. The outer regions of the galaxies' halos were assembled through pure accretion and disruption of satellites. Most of the in situ halo stars formed at high redshift out of smoothly accreted cold gas in the inner 1 kpc of the galaxies' potential wells, possibly as part of their primordial disks. These stars were displaced from their central locations into the halos through a succession of major mergers. We find that the two galaxies with recently quiescent merger histories have a higher fraction of in situ stars ({approx}20%-50%) in their inner halos than the two galaxies with many recent mergers ({approx}5%-10% in situ fraction). Observational studies concentrating on stellar populations in the inner halo of the Milky Way will be the most affected by the presence of in situ stars with halo kinematics, as we find that their existence in the inner few tens of kpc is a generic feature of galaxy formation.« less

Reconstruction of halo power spectrum from redshift-space galaxy distribution: cylinder-grouping method and halo exclusion effect

NASA Astrophysics Data System (ADS)

Okumura, Teppei; Takada, Masahiro; More, Surhud; Masaki, Shogo

2017-07-01

The peculiar velocity field measured by redshift-space distortions (RSD) in galaxy surveys provides a unique probe of the growth of large-scale structure. However, systematic effects arise when including satellite galaxies in the clustering analysis. Since satellite galaxies tend to reside in massive haloes with a greater halo bias, the inclusion boosts the clustering power. In addition, virial motions of the satellite galaxies cause a significant suppression of the clustering power due to non-linear RSD effects. We develop a novel method to recover the redshift-space power spectrum of haloes from the observed galaxy distribution by minimizing the contamination of satellite galaxies. The cylinder-grouping method (CGM) we study effectively excludes satellite galaxies from a galaxy sample. However, we find that this technique produces apparent anisotropies in the reconstructed halo distribution over all the scales which mimic RSD. On small scales, the apparent anisotropic clustering is caused by exclusion of haloes within the anisotropic cylinder used by the CGM. On large scales, the misidentification of different haloes in the large-scale structures, aligned along the line of sight, into the same CGM group causes the apparent anisotropic clustering via their cross-correlation with the CGM haloes. We construct an empirical model for the CGM halo power spectrum, which includes correction terms derived using the CGM window function at small scales as well as the linear matter power spectrum multiplied by a simple anisotropic function at large scales. We apply this model to a mock galaxy catalogue at z = 0.5, designed to resemble Sloan Digital Sky Survey-III Baryon Oscillation Spectroscopic Survey (BOSS) CMASS galaxies, and find that our model can predict both the monopole and quadrupole power spectra of the host haloes up to k < 0.5 {{h Mpc^{-1}}} to within 5 per cent.

Alignment of Common Wheat and Other Grass Genomes Establishes a Comparative Genomics Research Platform

PubMed Central

Sun, Sangrong; Wang, Jinpeng; Yu, Jigao; Meng, Fanbo; Xia, Ruiyan; Wang, Li; Wang, Zhenyi; Ge, Weina; Liu, Xiaojian; Li, Yuxian; Liu, Yinzhe; Yang, Nanshan; Wang, Xiyin

2017-01-01

Grass genomes are complicated structures as they share a common tetraploidization, and particular genomes have been further affected by extra polyploidizations. These events and the following genomic re-patternings have resulted in a complex, interweaving gene homology both within a genome, and between genomes. Accurately deciphering the structure of these complicated plant genomes would help us better understand their compositional and functional evolution at multiple scales. Here, we build on our previous research by performing a hierarchical alignment of the common wheat genome vis-à-vis eight other sequenced grass genomes with most up-to-date assemblies, and annotations. With this data, we constructed a list of the homologous genes, and then, in a layer-by-layer process, separated their orthology, and paralogy that were established by speciations and recursive polyploidizations, respectively. Compared with the other grasses, the far fewer collinear outparalogous genes within each of three subgenomes of common wheat suggest that homoeologous recombination, and genomic fractionation should have occurred after its formation. In sum, this work contributes to the establishment of an important and timely comparative genomics platform for researchers in the grass community and possibly beyond. Homologous gene list can be found in Supplemental material. PMID:28912789

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

PubMed

Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

2016-01-04

The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genome-wide comparative analysis of four Indian Drosophila species.

PubMed

Mohanty, Sujata; Khanna, Radhika

2017-12-01

Comparative analysis of multiple genomes of closely or distantly related Drosophila species undoubtedly creates excitement among evolutionary biologists in exploring the genomic changes with an ecology and evolutionary perspective. We present herewith the de novo assembled whole genome sequences of four Drosophila species, D. bipectinata, D. takahashii, D. biarmipes and D. nasuta of Indian origin using Next Generation Sequencing technology on an Illumina platform along with their detailed assembly statistics. The comparative genomics analysis, e.g. gene predictions and annotations, functional and orthogroup analysis of coding sequences and genome wide SNP distribution were performed. The whole genome of Zaprionus indianus of Indian origin published earlier by us and the genome sequences of previously sequenced 12 Drosophila species available in the NCBI database were included in the analysis. The present work is a part of our ongoing genomics project of Indian Drosophila species.

Connecting massive galaxies to dark matter haloes in BOSS - I. Is galaxy colour a stochastic process in high-mass haloes?

NASA Astrophysics Data System (ADS)

Saito, Shun; Leauthaud, Alexie; Hearin, Andrew P.; Bundy, Kevin; Zentner, Andrew R.; Behroozi, Peter S.; Reid, Beth A.; Sinha, Manodeep; Coupon, Jean; Tinker, Jeremy L.; White, Martin; Schneider, Donald P.

2016-08-01

We use subhalo abundance matching (SHAM) to model the stellar mass function (SMF) and clustering of the Baryon Oscillation Spectroscopic Survey (BOSS) `CMASS' sample at z ˜ 0.5. We introduce a novel method which accounts for the stellar mass incompleteness of CMASS as a function of redshift, and produce CMASS mock catalogues which include selection effects, reproduce the overall SMF, the projected two-point correlation function wp, the CMASS dn/dz, and are made publicly available. We study the effects of assembly bias above collapse mass in the context of `age matching' and show that these effects are markedly different compared to the ones explored by Hearin et al. at lower stellar masses. We construct two models, one in which galaxy colour is stochastic (`AbM' model) as well as a model which contains assembly bias effects (`AgM' model). By confronting the redshift dependent clustering of CMASS with the predictions from our model, we argue that that galaxy colours are not a stochastic process in high-mass haloes. Our results suggest that the colours of galaxies in high-mass haloes are determined by other halo properties besides halo peak velocity and that assembly bias effects play an important role in determining the clustering properties of this sample.

Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes.

PubMed

Sun, Yan-Bo; Xiong, Zi-Jun; Xiang, Xue-Yan; Liu, Shi-Ping; Zhou, Wei-Wei; Tu, Xiao-Long; Zhong, Li; Wang, Lu; Wu, Dong-Dong; Zhang, Bao-Lin; Zhu, Chun-Ling; Yang, Min-Min; Chen, Hong-Man; Li, Fang; Zhou, Long; Feng, Shao-Hong; Huang, Chao; Zhang, Guo-Jie; Irwin, David; Hillis, David M; Murphy, Robert W; Yang, Huan-Ming; Che, Jing; Wang, Jun; Zhang, Ya-Ping

2015-03-17

The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

WEIGHING THE GALACTIC DARK MATTER HALO: A LOWER MASS LIMIT FROM THE FASTEST HALO STAR KNOWN

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

Przybilla, Norbert; Tillich, Alfred; Heber, Ulrich

2010-07-20

The mass of the Galactic dark matter halo is under vivid discussion. A recent study by Xue et al. revised the Galactic halo mass downward by a factor of {approx}2 relative to previous work, based on the line-of-sight velocity distribution of {approx}2400 blue horizontal-branch (BHB) halo stars. The observations were interpreted with a statistical approach using cosmological galaxy formation simulations, as only four of the six-dimensional phase-space coordinates were determined. Here we concentrate on a close investigation of the stars with the highest negative radial velocity from that sample. For one star, SDSSJ153935.67+023909.8 (J1539+0239 for short), we succeed in measuringmore » a significant proper motion, i.e., full phase-space information is obtained. We confirm the star to be a Population II BHB star from an independent quantitative analysis of the Sloan Digital Sky Survey (SDSS) spectrum-providing the first non-LTE (NLTE) study of any halo BHB star-and reconstruct its three-dimensional trajectory in the Galactic potential. J1539+0239 turns out to be the fastest halo star known to date, with a Galactic rest-frame velocity of 694{sup +300}{sub -221} km s{sup -1} (full uncertainty range from Monte Carlo error propagation) at its current position. The extreme kinematics of the star allows a significant lower limit to be put on the halo mass in order to keep it bound, of M {sub halo} {>=} 1.7{sup +2.3}{sub -1.1} x 10{sup 12} M{sub sun}. We conclude that the Xue et al. results tend to underestimate the true halo mass as their most likely mass value is consistent with our analysis only at a level of 4%. However, our result confirms other studies that make use of the full phase-space information.« less

Is the Milky Way's hot halo convectively unstable?

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

Henley, David B.; Shelton, Robin L., E-mail: dbh@physast.uga.edu

2014-03-20

We investigate the convective stability of two popular types of model of the gas distribution in the hot Galactic halo. We first consider models in which the halo density and temperature decrease exponentially with height above the disk. These halo models were created to account for the fact that, on some sight lines, the halo's X-ray emission lines and absorption lines yield different temperatures, implying that the halo is non-isothermal. We show that the hot gas in these exponential models is convectively unstable if γ < 3/2, where γ is the ratio of the temperature and density scale heights. Usingmore » published measurements of γ and its uncertainty, we use Bayes' theorem to infer posterior probability distributions for γ, and hence the probability that the halo is convectively unstable for different sight lines. We find that, if these exponential models are good descriptions of the hot halo gas, at least in the first few kiloparsecs from the plane, the hot halo is reasonably likely to be convectively unstable on two of the three sight lines for which scale height information is available. We also consider more extended models of the halo. While isothermal halo models are convectively stable if the density decreases with distance from the Galaxy, a model of an extended adiabatic halo in hydrostatic equilibrium with the Galaxy's dark matter is on the boundary between stability and instability. However, we find that radiative cooling may perturb this model in the direction of convective instability. If the Galactic halo is indeed convectively unstable, this would argue in favor of supernova activity in the Galactic disk contributing to the heating of the hot halo gas.« less

Gramene 2016: comparative plant genomics and pathway resources

PubMed Central

Tello-Ruiz, Marcela K.; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M.; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A.; Huerta, Laura; Keays, Maria; Tang, Y. Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J.; Jaiswal, Pankaj; Ware, Doreen

2016-01-01

Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials. PMID:26553803

Sockeye: A 3D Environment for Comparative Genomics

PubMed Central

Montgomery, Stephen B.; Astakhova, Tamara; Bilenky, Mikhail; Birney, Ewan; Fu, Tony; Hassel, Maik; Melsopp, Craig; Rak, Marcin; Robertson, A. Gordon; Sleumer, Monica; Siddiqui, Asim S.; Jones, Steven J.M.

2004-01-01

Comparative genomics techniques are used in bioinformatics analyses to identify the structural and functional properties of DNA sequences. As the amount of available sequence data steadily increases, the ability to perform large-scale comparative analyses has become increasingly relevant. In addition, the growing complexity of genomic feature annotation means that new approaches to genomic visualization need to be explored. We have developed a Java-based application called Sockeye that uses three-dimensional (3D) graphics technology to facilitate the visualization of annotation and conservation across multiple sequences. This software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization. PMID:15123592

Concentrations of Simulated Dark Matter Halos

NASA Astrophysics Data System (ADS)

Child, Hillary

2017-01-01

We present the concentration-mass (c-M) relation of dark matter halos in two new high-volume high-resolution cosmological N-body simulations, Q Continuum and Outer Rim. Concentration describes the density of the central regions of halos; it is highest for low-mass halos at low redshift, decreasing at high mass and redshift. The shape of the c-M relation is an important probe of cosmology. We discuss the redshift dependence of the c-M relation, several different methods to determine concentrations of simulated halos, and potential sources of bias in concentration measurements. To connect to lensing observations, we stack halos, which also allows us to assess the suitability of the Navarro-Frenk-White profile and other profiles, such as Einasto, with an additional shape parameter. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-1144082.

Unbound particles in dark matter halos

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

Behroozi, Peter S.; Wechsler, Risa H.; Loeb, Abraham, E-mail: behroozi@stanford.edu, E-mail: aloeb@cfa.harvard.edu, E-mail: rwechsler@stanford.edu

2013-06-01

We investigate unbound dark matter particles in halos by tracing particle trajectories in a simulation run to the far future (a = 100). We find that the traditional sum of kinetic and potential energies is a very poor predictor of which dark matter particles will eventually become unbound from halos. We also study the mass fraction of unbound particles, which increases strongly towards the edges of halos, and decreases significantly at higher redshifts. We discuss implications for dark matter detection experiments, precision calibrations of the halo mass function, the use of baryon fractions to constrain dark energy, and searches formore » intergalactic supernovae.« less

Unbound particles in dark matter halos

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

Behroozi, Peter S.; Loeb, Abraham; Wechsler, Risa H.

2013-06-13

We investigate unbound dark matter particles in halos by tracing particle trajectories in a simulation run to the far future (a = 100). We find that the traditional sum of kinetic and potential energies is a very poor predictor of which dark matter particles will eventually become unbound from halos. We also study the mass fraction of unbound particles, which increases strongly towards the edges of halos, and decreases significantly at higher redshifts. We discuss implications for dark matter detection experiments, precision calibrations of the halo mass function, the use of baryon fractions to constrain dark energy, and searches formore » intergalactic supernovae.« less

Tests and consequences of disk plus halo models of gamma-ray burst sources

NASA Technical Reports Server (NTRS)

Smith, I. A.

1995-01-01

The gamma-ray burst observations made by the Burst and Transient Source Experiment (BATSE) and by previous experiments are still consistent with a combined Galactic disk (or Galactic spiral arm) plus extended Galactic halo model. Testable predictions and consequences of the disk plus halo model are discussed here; tests performed on the expanded BATSE database in the future will constrain the allowed model parameters and may eventually rule out the disk plus halo model. Using examples, it is shown that if the halo has an appropriate edge, BATSE will never detect an anisotropic signal from the halo of the Andromeda galaxy. A prediction of the disk plus halo model is that the fraction of the bursts observed to be in the 'disk' population rises as the detector sensitivity improves. A careful reexamination of the numbers of bursts in the two populations for the pre-BATSE databases could rule out this class of models. Similarly, it is predicted that different satellites will observe different relative numbers of bursts in the two classes for any model in which there are two different spatial distribiutions of the sources, or for models in which there is one spatial distribution of the sources that is sampled to different depths for the two classes. An important consequence of the disk plus halo model is that for the birthrate of the halo sources to be small compared to the birthrate of the disk sources, it is necessary for the halo sources to release many orders of magnitude more energy over their bursting lifetime than the disk sources. The halo bursts must also be much more luminous than the disk bursts; if this disk-halo model is correct, it is necessary to explain why the disk sources do not produce halo-type bursts.

Effective field theory description of halo nuclei

NASA Astrophysics Data System (ADS)

Hammer, H.-W.; Ji, C.; Phillips, D. R.

2017-10-01

Nuclear halos emerge as new degrees of freedom near the neutron and proton driplines. They consist of a core and one or a few nucleons which spend most of their time in the classically-forbidden region outside the range of the interaction. Individual nucleons inside the core are thus unresolved in the halo configuration, and the low-energy effective interactions are short-range forces between the core and the valence nucleons. Similar phenomena occur in clusters of 4He atoms, cold atomic gases near a Feshbach resonance, and some exotic hadrons. In these weakly-bound quantum systems universal scaling laws for s-wave binding emerge that are independent of the details of the interaction. Effective field theory (EFT) exposes these correlations and permits the calculation of non-universal corrections to them due to short-distance effects, as well as the extension of these ideas to systems involving the Coulomb interaction and/or binding in higher angular-momentum channels. Halo nuclei exhibit all these features. Halo EFT, the EFT for halo nuclei, has been used to compute the properties of single-neutron, two-neutron, and single-proton halos of s-wave and p-wave type. This review summarizes these results for halo binding energies, radii, Coulomb dissociation, and radiative capture, as well as the connection of these properties to scattering parameters, thereby elucidating the universal correlations between all these observables. We also discuss how Halo EFT's encoding of the long-distance physics of halo nuclei can be used to check and extend ab initio calculations that include detailed modeling of their short-distance dynamics.

Cosmic Vorticity and the Origin Halo Spins

NASA Astrophysics Data System (ADS)

Libeskind, Noam I.; Hoffman, Yehuda; Steinmetz, Matthias; Gottlöber, Stefan; Knebe, Alexander; Hess, Steffen

2013-04-01

In the standard model of cosmology, structure emerges out of a non-rotational flow and the angular momentum of collapsing halos is induced by tidal torques. The growth of angular momentum in the linear and quasi-linear phases is associated with a shear, curl-free, flow and it is well described within the linear framework of tidal torque theory (TTT). However, TTT ceases to be applicable as halos approach turnaround when their ambient flow field becomes rotational. Subsequently, halos become embedded in a vortical flow field and the growth of their angular momentum is affected by the vorticity of their ambient velocity field. Using a cosmological simulation, we have examined the importance of the curl of the velocity field in determining halo spin, finding a significant alignment between the two: the vorticity tends to be perpendicular to the axis of the fastest collapse of the velocity shear tensor (e 1). This is independent of halo masses and cosmic web environment. Our results agree with previous findings on the tendency of halo spin to be perpendicular to e 1, and of the spin of (simulated) halos and (observed) galaxies to be aligned with the large-scale structure. It follows that angular momentum growth proceeds in two distinct phases. First, the angular momentum emerges out of a shear, curl-free, potential flow, as described by TTT. In the second phase, in which halos approach virialization, the angular momentum emerges out of a vortical flow and halo spin becomes partially aligned with the vorticity of the ambient flow field.

Sinbase: an integrated database to study genomics, genetics and comparative genomics in Sesamum indicum.

PubMed

Wang, Linhai; Yu, Jingyin; Li, Donghua; Zhang, Xiurong

2015-01-01

Sesame (Sesamum indicum L.) is an ancient and important oilseed crop grown widely in tropical and subtropical areas. It belongs to the gigantic order Lamiales, which includes many well-known or economically important species, such as olive (Olea europaea), leonurus (Leonurus japonicus) and lavender (Lavandula spica), many of which have important pharmacological properties. Despite their importance, genetic and genomic analyses on these species have been insufficient due to a lack of reference genome information. The now available S. indicum genome will provide an unprecedented opportunity for studying both S. indicum genetic traits and comparative genomics. To deliver S. indicum genomic information to the worldwide research community, we designed Sinbase, a web-based database with comprehensive sesame genomic, genetic and comparative genomic information. Sinbase includes sequences of assembled sesame pseudomolecular chromosomes, protein-coding genes (27,148), transposable elements (372,167) and non-coding RNAs (1,748). In particular, Sinbase provides unique and valuable information on colinear regions with various plant genomes, including Arabidopsis thaliana, Glycine max, Vitis vinifera and Solanum lycopersicum. Sinbase also provides a useful search function and data mining tools, including a keyword search and local BLAST service. Sinbase will be updated regularly with new features, improvements to genome annotation and new genomic sequences, and is freely accessible at http://ocri-genomics.org/Sinbase/. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Dark matter haloes: a multistream view

NASA Astrophysics Data System (ADS)

Ramachandra, Nesar S.; Shandarin, Sergei F.

2017-09-01

Mysterious dark matter constitutes about 85 per cent of all masses in the Universe. Clustering of dark matter plays a dominant role in the formation of all observed structures on scales from a fraction to a few hundreds of Mega-parsecs. Galaxies play a role of lights illuminating these structures so they can be observed. The observations in the last several decades have unveiled opulent geometry of these structures currently known as the cosmic web. Haloes are the highest concentrations of dark matter and host luminous galaxies. Currently the most accurate modelling of dark matter haloes is achieved in cosmological N-body simulations. Identifying the haloes from the distribution of particles in N-body simulations is one of the problems attracting both considerable interest and efforts. We propose a novel framework for detecting potential dark matter haloes using the field unique for dark matter-multistream field. The multistream field emerges at the non-linear stage of the growth of perturbations because the dark matter is collisionless. Counting the number of velocity streams in gravitational collapses supplements our knowledge of spatial clustering. We assume that the virialized haloes have convex boundaries. Closed and convex regions of the multistream field are hence isolated by imposing a positivity condition on all three eigenvalues of the Hessian estimated on the smoothed multistream field. In a single-scale analysis of high multistream field resolution and low softening length, the halo substructures with local multistream maxima are isolated as individual halo sites.

Moving-mesh cosmology: characteristics of galaxies and haloes

NASA Astrophysics Data System (ADS)

Kereš, Dušan; Vogelsberger, Mark; Sijacki, Debora; Springel, Volker; Hernquist, Lars

2012-09-01

We discuss cosmological hydrodynamic simulations of galaxy formation performed with the new moving-mesh code AREPO, which promises higher accuracy compared with the traditional smoothed particle hydrodynamics (SPH) technique that has been widely employed for this problem. In this exploratory study, we deliberately limit the complexity of the physical processes followed by the code for ease of comparison with previous calculations, and include only cooling of gas with a primordial composition, heating by a spatially uniform ultraviolet background, and a simple subresolution model for regulating star formation in the dense interstellar medium. We use an identical set of physics in corresponding simulations carried out with the well-tested SPH code GADGET, adopting also the same high-resolution gravity solver. We are thus able to compare both simulation sets on an object-by-object basis, allowing us to cleanly isolate the impact of different hydrodynamical methods on galaxy and halo properties. In accompanying papers, Vogelsberger et al. and Sijacki et al., we focus on an analysis of the global baryonic statistics predicted by the simulation codes, and complementary idealized simulations that highlight the differences between the hydrodynamical schemes. Here we investigate their influence on the baryonic properties of simulated galaxies and their surrounding haloes. We find that AREPO leads to significantly higher star formation rates for galaxies in massive haloes and to more extended gaseous discs in galaxies, which also feature a thinner and smoother morphology than their GADGET counterparts. Consequently, galaxies formed in AREPO have larger sizes and higher specific angular momentum than their SPH correspondents. Interestingly, the more efficient cooling flows in AREPO yield higher densities and lower entropies in halo centres compared to GADGET, whereas the opposite trend is found in halo outskirts. The cooling differences leading to higher star formation rates

Effect of halo-vest components on stabilizing the injured cervical spine.

PubMed

Ivancic, Paul C; Beauchman, Naseem N; Tweardy, Lisa

2009-01-15

An in vitro biomechanical study. The objectives were to develop a new biofidelic skull-neck-thorax model capable of quantifying motion patterns of the cervical spine in the presence of a halo-vest; to investigate the effects of vest loosening, superstructure loosening, and removal of the posterior uprights; and to evaluate the ability of the halo-vest to stabilize the neck within physiological motion limits. Previous clinical and biomechanical studies have investigated neck motion with the halo-vest only in the sagittal plane or only at the injured spinal level. No previous studies have quantified three-dimensional intervertebral motion patterns throughout the injured cervical spine stabilized with the halo-vest or studied the effect of halo-vest components on these motions. The halo-vest was applied to the skull-neck-thorax model. Six osteoligamentous whole cervical spine specimens (occiput through T1 vertebra) were used that had sustained multiplanar ligamentous injuries at C3/4 through C7-T1 during a previous protocol. Flexibility tests were performed with normal halo-vest application, loose vest, loose superstructure, and following removal of the posterior uprights. Average total range of motion for each experimental condition was statistically compared (P < 0.05) with the physiologic rotation limit for each spinal level. Cervical spine snaking was observed in both the sagittal and frontal planes. The halo-vest, applied normally, generally limited average spinal motions to within average physiological limits. No significant increases in average spinal motions above physiologic were observed due to loose vest, loose superstructure, or removal of the posterior uprights. However, a trend toward increased motion at C6/7 in lateral bending was observed due to loose superstructure. The halo-vest, applied normally, effectively immobilized the cervical spine. Sagittal or frontal plane snaking of the cervical spine due to the halo-vest may reduce its immobilization

The HALO / HALO-2 Supernova Neutrino Detectors

NASA Astrophysics Data System (ADS)

Yen, Stanley; HALO Collaboration; HALO-2 Collaboration

2016-09-01

The Helium and Lead Observatory (HALO) is a dedicated supernova neutrino detector in SNOLAB, which is built from 79 tons of surplus lead and the helium-3 neutron detectors from the SNO experiment. It is sensitive primarily to electron neutrinos, and is thus complementary to water Cerenkov and organic scintillation detectors which are primarily sensitive to electron anti-neutrinos. A comparison of the rates in these complementary detectors will enable a flavor decomposition of the neutrino flux from the next galactic core-collapse supernova. We have tentative ideas to build a 1000-ton HALO-2 detector in the Gran Sasso laboratory by using the lead from the decommissioned OPERA detector. We are exploring several neutron detector technologies to supplement the existing helium-3 detectors. We welcome new collaborators to join us. This research is supported by the NRC and NSERC (Canada), the US DOE and NSF, and the German RISE program.

ZOMG - II. Does the halo assembly history influence central galaxies and gas accretion?

NASA Astrophysics Data System (ADS)

Romano-Díaz, Emilio; Garaldi, Enrico; Borzyszkowski, Mikolaj; Porciani, Cristiano

2017-08-01

The growth rate and the internal dynamics of galaxy-sized dark-matter haloes depend on their location within the cosmic web. Haloes that sit at the nodes grow in mass till the present time and are dominated by radial orbits. Conversely, haloes embedded in prominent filaments do not change much in size and are dominated by tangential orbits. Using zoom hydrodynamical simulations including star formation and feedback, we study how gas accretes on to these different classes of objects, which, for simplicity, we dub 'accreting' and 'stalled' haloes. We find that all haloes get a fresh supply of newly accreted gas in their inner regions, although this slowly decreases with time, in particular for the stalled haloes. The inflow of new gas is always higher than (but comparable with) that of recycled material. Overall, the cold-gas fraction increases (decreases) with time for the accreting (stalled) haloes. In all cases, a stellar disc and a bulge form at the centre of the simulated haloes. The total stellar mass is in excellent agreement with expectations based on the abundance-matching technique. Many properties of the central galaxies do not seem to correlate with the large-scale environment in which the haloes reside. However, there are two notable exceptions that characterize stalled haloes with respect to their accreting counterparts: (I) The galaxy disc contains much older stellar populations. (II) Its vertical scaleheight is larger by a factor of 2 or more. This thickening is likely due to the heating of the long-lived discs by mergers and close flybys.

FASTPM: a new scheme for fast simulations of dark matter and haloes

NASA Astrophysics Data System (ADS)

Feng, Yu; Chu, Man-Yat; Seljak, Uroš; McDonald, Patrick

2016-12-01

We introduce FASTPM, a highly scalable approximated particle mesh (PM) N-body solver, which implements the PM scheme enforcing correct linear displacement (1LPT) evolution via modified kick and drift factors. Employing a two-dimensional domain decomposing scheme, FASTPM scales extremely well with a very large number of CPUs. In contrast to Comoving-Lagrangian (COLA) approach, we do not require to split the force or track separately the 2LPT solution, reducing the code complexity and memory requirements. We compare FASTPM with different number of steps (Ns) and force resolution factor (B) against three benchmarks: halo mass function from friends-of-friends halo finder; halo and dark matter power spectrum; and cross-correlation coefficient (or stochasticity), relative to a high-resolution TREEPM simulation. We show that the modified time stepping scheme reduces the halo stochasticity when compared to COLA with the same number of steps and force resolution. While increasing Ns and B improves the transfer function and cross-correlation coefficient, for many applications FASTPM achieves sufficient accuracy at low Ns and B. For example, Ns = 10 and B = 2 simulation provides a substantial saving (a factor of 10) of computing time relative to Ns = 40, B = 3 simulation, yet the halo benchmarks are very similar at z = 0. We find that for abundance matched haloes the stochasticity remains low even for Ns = 5. FASTPM compares well against less expensive schemes, being only 7 (4) times more expensive than 2LPT initial condition generator for Ns = 10 (Ns = 5). Some of the applications where FASTPM can be useful are generating a large number of mocks, producing non-linear statistics where one varies a large number of nuisance or cosmological parameters, or serving as part of an initial conditions solver.

Smooth halos in the cosmic web

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

Gaite, José, E-mail: jose.gaite@upm.es

Dark matter halos can be defined as smooth distributions of dark matter placed in a non-smooth cosmic web structure. This definition of halos demands a precise definition of smoothness and a characterization of the manner in which the transition from smooth halos to the cosmic web takes place. We introduce entropic measures of smoothness, related to measures of inequality previously used in economy and with the advantage of being connected with standard methods of multifractal analysis already used for characterizing the cosmic web structure in cold dark matter N-body simulations. These entropic measures provide us with a quantitative description ofmore » the transition from the small scales portrayed as a distribution of halos to the larger scales portrayed as a cosmic web and, therefore, allow us to assign definite sizes to halos. However, these ''smoothness sizes'' have no direct relation to the virial radii. Finally, we discuss the influence of N-body discreteness parameters on smoothness.« less

Comparative genomics of Lactobacillus

PubMed Central

Kant, Ravi; Blom, Jochen; Palva, Airi; Siezen, Roland J.; de Vos, Willem M.

2011-01-01

Summary The genus Lactobacillus includes a diverse group of bacteria consisting of many species that are associated with fermentations of plants, meat or milk. In addition, various lactobacilli are natural inhabitants of the intestinal tract of humans and other animals. Finally, several Lactobacillus strains are marketed as probiotics as their consumption can confer a health benefit to host. Presently, 154 Lactobacillus species are known and a growing fraction of these are subject to draft genome sequencing. However, complete genome sequences are needed to provide a platform for detailed genomic comparisons. Therefore, we selected a total of 20 genomes of various Lactobacillus strains for which complete genomic sequences have been reported. These genomes had sizes varying from 1.8 to 3.3 Mb and other characteristic features, such as G+C content that ranged from 33% to 51%. The Lactobacillus pan genome was found to consist of approximately 14 000 protein‐encoding genes while all 20 genomes shared a total of 383 sets of orthologous genes that defined the Lactobacillus core genome (LCG). Based on advanced phylogeny of the proteins encoded by this LCG, we grouped the 20 strains into three main groups and defined core group genes present in all genomes of a single group, signature group genes shared in all genomes of one group but absent in all other Lactobacillus genomes, and Group‐specific ORFans present in core group genes of one group and absent in all other complete genomes. The latter are of specific value in defining the different groups of genomes. The study provides a platform for present individual comparisons as well as future analysis of new Lactobacillus genomes. PMID:21375712

Neck motion due to the halo-vest in prone and supine positions.

PubMed

Ivancic, Paul C; Telles, Connor J

2010-05-01

An in vitro biomechanical study of the effectiveness of halo-vest fixation. The objective was to evaluate motion of the injured cervical spine with normal halo-vest application and vest loose in the prone and supine positions. Snaking motion of the neck is defined as rotation in opposing directions throughout the cervical spine. Previous clinical studies have suggested snaking neck motion due to the halo-vest may lead to inadequate healing or nonunion. The halo-vest was applied to a Human Model of the Neck, which consisted of a cervical spine specimen mounted to the torso of an anthropometric test dummy and carrying a surrogate head. The model was transitioned from prone, to upright, to supine with the halo-vest applied normally and with the vest loose. Average peak spinal motions were computed in the prone and supine positions and contrasted with the physiologic rotation range, obtained from the intact flexibility test, and statistically compared (P < 0.05) between normal halo-vest application and vest loose. Snaking motion of the neck was observed in the prone and supine positions, consisting of extension at head/C1 and C1/2 and flexion at the inferior spinal levels. The intervertebral rotation peaks generally exceeded the physiologic range throughout the cervical spine due to the loose vest in the prone position. Significant increases in the extension peaks at head/C1 (16.9 degrees vs. 5.7 degrees) and flexion peaks at C4/5 (6.9 degrees vs. 3.6 degrees) and C7-T1 (5.2 degrees vs. 0.7 degrees) were observed in the prone position due to the loose vest, as compared to normal halo-vest application. Axial neck separation was consistently observed in the prone and supine positions. The present results, which document snaking motion of the cervical spine due to the halo-vest, indicate that an inadequately fitting or loose vest may significantly diminish its immobilization capacity leading to delayed healing or nonunion.

Comparative genomics meets topology: a novel view on genome median and halving problems.

PubMed

Alexeev, Nikita; Avdeyev, Pavel; Alekseyev, Max A

2016-11-11

Genome median and genome halving are combinatorial optimization problems that aim at reconstruction of ancestral genomes by minimizing the number of evolutionary events between them and genomes of the extant species. While these problems have been widely studied in past decades, their solutions are often either not efficient or not biologically adequate. These shortcomings have been recently addressed by restricting the problems solution space. We show that the restricted variants of genome median and halving problems are, in fact, closely related. We demonstrate that these problems have a neat topological interpretation in terms of embedded graphs and polygon gluings. We illustrate how such interpretation can lead to solutions to these problems in particular cases. This study provides an unexpected link between comparative genomics and topology, and demonstrates advantages of solving genome median and halving problems within the topological framework.

Comparative Genomics and Host Resistance against Infectious Diseases

PubMed Central

Qureshi, Salman T.; Skamene, Emil

1999-01-01

The large size and complexity of the human genome have limited the identification and functional characterization of components of the innate immune system that play a critical role in front-line defense against invading microorganisms. However, advances in genome analysis (including the development of comprehensive sets of informative genetic markers, improved physical mapping methods, and novel techniques for transcript identification) have reduced the obstacles to discovery of novel host resistance genes. Study of the genomic organization and content of widely divergent vertebrate species has shown a remarkable degree of evolutionary conservation and enables meaningful cross-species comparison and analysis of newly discovered genes. Application of comparative genomics to host resistance will rapidly expand our understanding of human immune defense by facilitating the translation of knowledge acquired through the study of model organisms. We review the rationale and resources for comparative genomic analysis and describe three examples of host resistance genes successfully identified by this approach. PMID:10081670

Gramene 2013: comparative plant genomics resources.

PubMed

Monaco, Marcela K; Stein, Joshua; Naithani, Sushma; Wei, Sharon; Dharmawardhana, Palitha; Kumari, Sunita; Amarasinghe, Vindhya; Youens-Clark, Ken; Thomason, James; Preece, Justin; Pasternak, Shiran; Olson, Andrew; Jiao, Yinping; Lu, Zhenyuan; Bolser, Dan; Kerhornou, Arnaud; Staines, Dan; Walts, Brandon; Wu, Guanming; D'Eustachio, Peter; Haw, Robin; Croft, David; Kersey, Paul J; Stein, Lincoln; Jaiswal, Pankaj; Ware, Doreen

2014-01-01

Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology.

Using comparative genome analysis to identify problems in annotated microbial genomes.

PubMed

Poptsova, Maria S; Gogarten, J Peter

2010-07-01

Genome annotation is a tedious task that is mostly done by automated methods; however, the accuracy of these approaches has been questioned since the beginning of the sequencing era. Genome annotation is a multilevel process, and errors can emerge at different stages: during sequencing, as a result of gene-calling procedures, and in the process of assigning gene functions. Missed or wrongly annotated genes differentially impact different types of analyses. Here we discuss and demonstrate how the methods of comparative genome analysis can refine annotations by locating missing orthologues. We also discuss possible reasons for errors and show that the second-generation annotation systems, which combine multiple gene-calling programs with similarity-based methods, perform much better than the first annotation tools. Since old errors may propagate to the newly sequenced genomes, we emphasize that the problem of continuously updating popular public databases is an urgent and unresolved one. Due to the progress in genome-sequencing technologies, automated annotation techniques will remain the main approach in the future. Researchers need to be aware of the existing errors in the annotation of even well-studied genomes, such as Escherichia coli, and consider additional quality control for their results.

Whole genomic DNA sequencing and comparative genomic analysis of Arthrospira platensis: high genome plasticity and genetic diversity

PubMed Central

Xu, Teng; Qin, Song; Hu, Yongwu; Song, Zhijian; Ying, Jianchao; Li, Peizhen; Dong, Wei; Zhao, Fangqing; Yang, Huanming; Bao, Qiyu

2016-01-01

Arthrospira platensis is a multi-cellular and filamentous non-N2-fixing cyanobacterium that is capable of performing oxygenic photosynthesis. In this study, we determined the nearly complete genome sequence of A. platensis YZ. A. platensis YZ genome is a single, circular chromosome of 6.62 Mb in size. Phylogenetic and comparative genomic analyses revealed that A. platensis YZ was more closely related to A. platensis NIES-39 than Arthrospira sp. PCC 8005 and A. platensis C1. Broad gene gains were identified between A. platensis YZ and three other Arthrospira speices, some of which have been previously demonstrated that can be laterally transferred among different species, such as restriction-modification systems-coding genes. Moreover, unprecedented extensive chromosomal rearrangements among different strains were observed. The chromosomal rearrangements, particularly the chromosomal inversions, were analysed and estimated to be closely related to palindromes that involved long inverted repeat sequences and the extensively distributed type IIR restriction enzyme in the Arthrospira genome. In addition, species from genus Arthrospira unanimously contained the highest rate of repetitive sequence compared with the other species of order Oscillatoriales, suggested that sequence duplication significantly contributed to Arthrospira genome phylogeny. These results provided in-depth views into the genomic phylogeny and structural variation of A. platensis, as well as provide a valuable resource for functional genomics studies. PMID:27330141

Low-pass sequencing for microbial comparative genomics

PubMed Central

Goo, Young Ah; Roach, Jared; Glusman, Gustavo; Baliga, Nitin S; Deutsch, Kerry; Pan, Min; Kennedy, Sean; DasSarma, Shiladitya; Victor Ng, Wailap; Hood, Leroy

2004-01-01

Background We studied four extremely halophilic archaea by low-pass shotgun sequencing: (1) the metabolically versatile Haloarcula marismortui; (2) the non-pigmented Natrialba asiatica; (3) the psychrophile Halorubrum lacusprofundi and (4) the Dead Sea isolate Halobaculum gomorrense. Approximately one thousand single pass genomic sequences per genome were obtained. The data were analyzed by comparative genomic analyses using the completed Halobacterium sp. NRC-1 genome as a reference. Low-pass shotgun sequencing is a simple, inexpensive, and rapid approach that can readily be performed on any cultured microbe. Results As expected, the four archaeal halophiles analyzed exhibit both bacterial and eukaryotic characteristics as well as uniquely archaeal traits. All five halophiles exhibit greater than sixty percent GC content and low isoelectric points (pI) for their predicted proteins. Multiple insertion sequence (IS) elements, often involved in genome rearrangements, were identified in H. lacusprofundi and H. marismortui. The core biological functions that govern cellular and genetic mechanisms of H. sp. NRC-1 appear to be conserved in these four other halophiles. Multiple TATA box binding protein (TBP) and transcription factor IIB (TFB) homologs were identified from most of the four shotgunned halophiles. The reconstructed molecular tree of all five halophiles shows a large divergence between these species, but with the closest relationship being between H. sp. NRC-1 and H. lacusprofundi. Conclusion Despite the diverse habitats of these species, all five halophiles share (1) high GC content and (2) low protein isoelectric points, which are characteristics associated with environmental exposure to UV radiation and hypersalinity, respectively. Identification of multiple IS elements in the genome of H. lacusprofundi and H. marismortui suggest that genome structure and dynamic genome reorganization might be similar to that previously observed in the IS-element rich

COSMIC VORTICITY AND THE ORIGIN HALO SPINS

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

Libeskind, Noam I.; Steinmetz, Matthias; Gottloeber, Stefan

2013-04-01

In the standard model of cosmology, structure emerges out of a non-rotational flow and the angular momentum of collapsing halos is induced by tidal torques. The growth of angular momentum in the linear and quasi-linear phases is associated with a shear, curl-free, flow and it is well described within the linear framework of tidal torque theory (TTT). However, TTT ceases to be applicable as halos approach turnaround when their ambient flow field becomes rotational. Subsequently, halos become embedded in a vortical flow field and the growth of their angular momentum is affected by the vorticity of their ambient velocity field.more » Using a cosmological simulation, we have examined the importance of the curl of the velocity field in determining halo spin, finding a significant alignment between the two: the vorticity tends to be perpendicular to the axis of the fastest collapse of the velocity shear tensor (e{sub 1}). This is independent of halo masses and cosmic web environment. Our results agree with previous findings on the tendency of halo spin to be perpendicular to e{sub 1}, and of the spin of (simulated) halos and (observed) galaxies to be aligned with the large-scale structure. It follows that angular momentum growth proceeds in two distinct phases. First, the angular momentum emerges out of a shear, curl-free, potential flow, as described by TTT. In the second phase, in which halos approach virialization, the angular momentum emerges out of a vortical flow and halo spin becomes partially aligned with the vorticity of the ambient flow field.« less

Halo Intrinsic Alignment: Dependence on Mass, Formation Time, and Environment

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

Xia, Qianli; Kang, Xi; Wang, Peng

In this paper we use high-resolution cosmological simulations to study halo intrinsic alignment and its dependence on mass, formation time, and large-scale environment. In agreement with previous studies using N -body simulations, it is found that massive halos have stronger alignment. For the first time, we find that for a given halo mass older halos have stronger alignment and halos in cluster regions also have stronger alignment than those in filaments. To model these dependencies, we extend the linear alignment model with inclusion of halo bias and find that the halo alignment with its mass and formation time dependence canmore » be explained by halo bias. However, the model cannot account for the environment dependence, as it is found that halo bias is lower in clusters and higher in filaments. Our results suggest that halo bias and environment are independent factors in determining halo alignment. We also study the halo alignment correlation function and find that halos are strongly clustered along their major axes and less clustered along the minor axes. The correlated halo alignment can extend to scales as large as 100 h {sup −1} Mpc, where its feature is mainly driven by the baryon acoustic oscillation effect.« less

Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis.

PubMed

Baby, Vincent; Lachance, Jean-Christophe; Gagnon, Jules; Lucier, Jean-François; Matteau, Dominick; Knight, Tom; Rodrigue, Sébastien

2018-01-01

The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, we have identified the core genome and open pangenome of this species. Our results show that all of the strains have approximately 80% of their gene content in common. Of the remaining 20%, 17% of the genes were found in multiple strains and 3% were unique to any given strain. On the basis of random transposon mutagenesis, we also estimated that ~290 out of 720 genes are essential for M. florum L1 in rich medium. We next evaluated different genome reduction scenarios for M. florum L1 by using gene conservation and essentiality data, as well as comparisons with the first working approximation of a minimal organism, Mycoplasma mycoides JCVI-syn3.0. Our results suggest that 409 of the 473 M. mycoides JCVI-syn3.0 genes have orthologs in M. florum L1. Conversely, 57 putatively essential M. florum L1 genes have no homolog in M. mycoides JCVI-syn3.0. This suggests differences in minimal genome compositions, even for these evolutionarily closely related bacteria. IMPORTANCE The last years have witnessed the development of whole-genome cloning and transplantation methods and the complete synthesis of entire chromosomes. Recently, the first minimal cell, Mycoplasma mycoides JCVI-syn3.0, was created. Despite these milestone achievements, several questions remain to be answered. For example, is the composition of minimal genomes virtually identical in phylogenetically related species? On the basis of comparative genomics and transposon mutagenesis, we investigated this question by using an alternative model, Mesoplasma florum, that is also amenable to genome reduction efforts. Our results suggest that the creation of additional minimal

COMPARISON OF COMPARATIVE GENOMIC HYBRIDIZATIONS TECHNOLOGIES ACROSS MICROARRAY PLATFORMS

EPA Science Inventory

Comparative Genomic Hybridization (CGH) measures DNA copy number differences between a reference genome and a test genome. The DNA samples are differentially labeled and hybridized to an immobilized substrate. In early CGH experiments, the DNA targets were hybridized to metaphase...

The dependence of halo mass on galaxy size at fixed stellar mass using weak lensing

NASA Astrophysics Data System (ADS)

Charlton, Paul J. L.; Hudson, Michael J.; Balogh, Michael L.; Khatri, Sumeet

2017-12-01

Stellar mass has been shown to correlate with halo mass, with non-negligible scatter. The stellar mass-size and luminosity-size relationships of galaxies also show significant scatter in galaxy size at fixed stellar mass. It is possible that, at fixed stellar mass and galaxy colour, the halo mass is correlated with galaxy size. Galaxy-galaxy lensing allows us to measure the mean masses of dark matter haloes for stacked samples of galaxies. We extend the analysis of the galaxies in the CFHTLenS catalogue by fitting single Sérsic surface brightness profiles to the lens galaxies in order to recover half-light radius values, allowing us to determine halo masses for lenses according to their size. Comparing our halo masses and sizes to baselines for that stellar mass yields a differential measurement of the halo mass-galaxy size relationship at fixed stellar mass, defined as Mh(M_{*}) ∝ r_{eff}^{η }(M_{*}). We find that, on average, our lens galaxies have an η = 0.42 ± 0.12, i.e. larger galaxies live in more massive dark matter haloes. The η is strongest for high-mass luminous red galaxies. Investigation of this relationship in hydrodynamical simulations suggests that, at a fixed M*, satellite galaxies have a larger η and greater scatter in the Mh and reff relationship compared to central galaxies.

Density- and luminosity-functions for UBV-photometric discand halo-stars in SA 54, compared with earlier RGU-results in this field

NASA Astrophysics Data System (ADS)

Fenkart, R.; Esin-Yilmaz, F.

1983-12-01

Space density- and luminosity-functions for the photometric halo- and disc-populations in the test-field SA 54 of the Basle Halo Program have been derived on the basis of UBV observations of the same 1377 stars used already for the corresponding RGU investigation by Fenkart (1968). The statistical method for separating the photometrically defined populations and for attributing absolute magnitudes to their members developed, described and first applied to SA 51 in RGU by Becker (1965) has been adapted for use in the UBV system. The (U-B, B- V) diagrams for consecutive intervals in apparent V-magnitude of figures 2a to f contain, contrary to what was first expected in this system, substantial numbers of stars in the < blanketing-region above and to the right of the late branch of the two-colour diagram main-sequence. The density-functions for different MVintervals within the overall interval < 3m, 7m> covered by this investigation for halo and disc are given in tables IIa and b, and plotted in figures 3 and 4, respectively. The corresponding luminosity-functions within the partial volume up to 1 kpc from the sun over the same overall MVinterval are given together with Glieses (1969) solar values for population I, in table III, and plotted in figure 5. The overall density-functions (3m ≦ MV ≦ 7m) for both populations can be and are compared with the corresponding ones (3m ≦ MG ≦ 8m) in RGU (last column in table II) in figures 6 and 7, for halo and disc, respectively. The coincidence of the density results between UBV and RGU is much better for both populations than the mean misidentification rate per system derived in section 5 would let us expect, suggesting a statistically fairly repartition of the misidentifications with respect to absolute magnitudes and distances.

The Outer Halos of Early-Type Galaxies

NASA Astrophysics Data System (ADS)

Gerhard, Ortwin; Arnaboldi, Magda; Longobardi, Alessia

2015-04-01

The outer halos of massive early-type galaxies (ETGs) are dark matter dominated and may have formed by accretion of smaller systems during galaxy evolution. Here a brief report is given of some recent work on the kinematics, angular momentum, and mass distributions of simulated ETG halos, and of corresponding properties of observed halos measured with planetary nebulae (PNe) as tracers. In the outermost regions of the Virgo-central galaxy M87, the PN data show that the stellar halo and the co-spatial intracluster light are distinct kinematic components.

Comparative genomics of biotechnologically important yeasts

PubMed Central

Riley, Robert; Haridas, Sajeet; Wolfe, Kenneth H.; Lopes, Mariana R.; Hittinger, Chris Todd; Göker, Markus; Salamov, Asaf A.; Wisecaver, Jennifer H.; Long, Tanya M.; Aerts, Andrea L.; Barry, Kerrie W.; Choi, Cindy; Clum, Alicia; Coughlan, Aisling Y.; Deshpande, Shweta; Douglass, Alexander P.; Hanson, Sara J.; Klenk, Hans-Peter; LaButti, Kurt M.; Lapidus, Alla; Lindquist, Erika A.; Lipzen, Anna M.; Meier-Kolthoff, Jan P.; Ohm, Robin A.; Otillar, Robert P.; Pangilinan, Jasmyn L.; Peng, Yi; Rosa, Carlos A.; Scheuner, Carmen; Sibirny, Andriy A.; Slot, Jason C.; Stielow, J. Benjamin; Sun, Hui; Kurtzman, Cletus P.; Blackwell, Meredith; Grigoriev, Igor V.

2016-01-01

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the clade sister to the known CUG-Ser clade. Our well-resolved yeast phylogeny shows that some traits, such as methylotrophy, are restricted to single clades, whereas others, such as l-rhamnose utilization, have patchy phylogenetic distributions. Gene clusters, with variable organization and distribution, encode many pathways of interest. Genomics can predict some biochemical traits precisely, but the genomic basis of others, such as xylose utilization, remains unresolved. Our data also provide insight into early evolution of ascomycetes. We document the loss of H3K9me2/3 heterochromatin, the origin of ascomycete mating-type switching, and panascomycete synteny at the MAT locus. These data and analyses will facilitate the engineering of efficient biosynthetic and degradative pathways and gateways for genomic manipulation. PMID:27535936

Gramene 2016: comparative plant genomics and pathway resources.

PubMed

Tello-Ruiz, Marcela K; Stein, Joshua; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; Elser, Justin; Wang, Bo; Thomason, James; Bolser, Daniel M; Kerhornou, Arnaud; Walts, Brandon; Fonseca, Nuno A; Huerta, Laura; Keays, Maria; Tang, Y Amy; Parkinson, Helen; Fabregat, Antonio; McKay, Sheldon; Weiser, Joel; D'Eustachio, Peter; Stein, Lincoln; Petryszak, Robert; Kersey, Paul J; Jaiswal, Pankaj; Ware, Doreen

2016-01-04

Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The genomes section features 39 fully assembled reference genomes that are integrated using ontology-based annotation and comparative analyses, and accessed through both visual and programmatic interfaces. Additional community data, such as genetic variation, expression and methylation, are also mapped for a subset of genomes. The Plant Reactome pathway portal (http://plantreactome.gramene.org) provides a reference resource for analyzing plant metabolic and regulatory pathways. In addition to ∼ 200 curated rice reference pathways, the portal hosts gene homology-based pathway projections for 33 plant species. Both the genome and pathway browsers interface with the EMBL-EBI's Expression Atlas to enable the projection of baseline and differential expression data from curated expression studies in plants. Gramene's archive website (http://archive.gramene.org) continues to provide previously reported resources on comparative maps, markers and QTL. To further aid our users, we have also introduced a live monthly educational webinar series and a Gramene YouTube channel carrying video tutorials. Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Alignments of Dark Matter Halos with Large-scale Tidal Fields: Mass and Redshift Dependence

NASA Astrophysics Data System (ADS)

Chen, Sijie; Wang, Huiyuan; Mo, H. J.; Shi, Jingjing

2016-07-01

Large-scale tidal fields estimated directly from the distribution of dark matter halos are used to investigate how halo shapes and spin vectors are aligned with the cosmic web. The major, intermediate, and minor axes of halos are aligned with the corresponding tidal axes, and halo spin axes tend to be parallel with the intermediate axes and perpendicular to the major axes of the tidal field. The strengths of these alignments generally increase with halo mass and redshift, but the dependence is only on the peak height, ν \\equiv {δ }{{c}}/σ ({M}{{h}},z). The scaling relations of the alignment strengths with the value of ν indicate that the alignment strengths remain roughly constant when the structures within which the halos reside are still in a quasi-linear regime, but decreases as nonlinear evolution becomes more important. We also calculate the alignments in projection so that our results can be compared directly with observations. Finally, we investigate the alignments of tidal tensors on large scales, and use the results to understand alignments of halo pairs separated at various distances. Our results suggest that the coherent structure of the tidal field is the underlying reason for the alignments of halos and galaxies seen in numerical simulations and in observations.

Sputnik: a database platform for comparative plant genomics.

PubMed

Rudd, Stephen; Mewes, Hans-Werner; Mayer, Klaus F X

2003-01-01

Two million plant ESTs, from 20 different plant species, and totalling more than one 1000 Mbp of DNA sequence, represents a formidable transcriptomic resource. Sputnik uses the potential of this sequence resource to fill some of the information gap in the un-sequenced plant genomes and to serve as the foundation for in silicio comparative plant genomics. The complexity of the individual EST collections has been reduced using optimised EST clustering techniques. Annotation of cluster sequences is performed by exploiting and transferring information from the comprehensive knowledgebase already produced for the completed model plant genome (Arabidopsis thaliana) and by performing additional state of-the-art sequence analyses relevant to today's plant biologist. Functional predictions, comparative analyses and associative annotations for 500 000 plant EST derived peptides make Sputnik (http://mips.gsf.de/proj/sputnik/) a valid platform for contemporary plant genomics.

Sputnik: a database platform for comparative plant genomics

PubMed Central

Rudd, Stephen; Mewes, Hans-Werner; Mayer, Klaus F.X.

2003-01-01

Two million plant ESTs, from 20 different plant species, and totalling more than one 1000 Mbp of DNA sequence, represents a formidable transcriptomic resource. Sputnik uses the potential of this sequence resource to fill some of the information gap in the un-sequenced plant genomes and to serve as the foundation for in silicio comparative plant genomics. The complexity of the individual EST collections has been reduced using optimised EST clustering techniques. Annotation of cluster sequences is performed by exploiting and transferring information from the comprehensive knowledgebase already produced for the completed model plant genome (Arabidopsis thaliana) and by performing additional state of-the-art sequence analyses relevant to today's plant biologist. Functional predictions, comparative analyses and associative annotations for 500 000 plant EST derived peptides make Sputnik (http://mips.gsf.de/proj/sputnik/) a valid platform for contemporary plant genomics. PMID:12519965

Comparative genomics of wild type yeast strains unveils important genome diversity

PubMed Central

Carreto, Laura; Eiriz, Maria F; Gomes, Ana C; Pereira, Patrícia M; Schuller, Dorit; Santos, Manuel AS

2008-01-01

Background Genome variability generates phenotypic heterogeneity and is of relevance for adaptation to environmental change, but the extent of such variability in natural populations is still poorly understood. For example, selected Saccharomyces cerevisiae strains are variable at the ploidy level, have gene amplifications, changes in chromosome copy number, and gross chromosomal rearrangements. This suggests that genome plasticity provides important genetic diversity upon which natural selection mechanisms can operate. Results In this study, we have used wild-type S. cerevisiae (yeast) strains to investigate genome variation in natural and artificial environments. We have used comparative genome hybridization on array (aCGH) to characterize the genome variability of 16 yeast strains, of laboratory and commercial origin, isolated from vineyards and wine cellars, and from opportunistic human infections. Interestingly, sub-telomeric instability was associated with the clinical phenotype, while Ty element insertion regions determined genomic differences of natural wine fermentation strains. Copy number depletion of ASP3 and YRF1 genes was found in all wild-type strains. Other gene families involved in transmembrane transport, sugar and alcohol metabolism or drug resistance had copy number changes, which also distinguished wine from clinical isolates. Conclusion We have isolated and genotyped more than 1000 yeast strains from natural environments and carried out an aCGH analysis of 16 strains representative of distinct genotype clusters. Important genomic variability was identified between these strains, in particular in sub-telomeric regions and in Ty-element insertion sites, suggesting that this type of genome variability is the main source of genetic diversity in natural populations of yeast. The data highlights the usefulness of yeast as a model system to unravel intraspecific natural genome diversity and to elucidate how natural selection shapes the yeast genome

Analytic halo approach to the bispectrum of galaxies in redshift space

NASA Astrophysics Data System (ADS)

Yamamoto, Kazuhiro; Nan, Yue; Hikage, Chiaki

2017-02-01

We present an analytic formula for the galaxy bispectrum in redshift space on the basis of the halo approach description with the halo occupation distribution of central galaxies and satellite galaxies. This work is an extension of a previous work on the galaxy power spectrum, which illuminated the significant contribution of satellite galaxies to the higher multipole spectrum through the nonlinear redshift space distortions of their random motions. Behaviors of the multipoles of the bispectrum are compared with results of numerical simulations assuming a halo occupation distribution of the low-redshift (LOWZ) sample of the Sloan Digital Sky Survey (SDSS) III baryon oscillation spectroscopic survey (BOSS) survey. Also presented are analytic approximate formulas for the multipoles of the bispectrum, which is useful to understanding their characteristic properties. We demonstrate that the Fingers of God effect is quite important for the higher multipoles of the bispectrum in redshift space, depending on the halo occupation distribution parameters.

CMG-biotools, a free workbench for basic comparative microbial genomics.

PubMed

Vesth, Tammi; Lagesen, Karin; Acar, Öncel; Ussery, David

2013-01-01

Today, there are more than a hundred times as many sequenced prokaryotic genomes than were present in the year 2000. The economical sequencing of genomic DNA has facilitated a whole new approach to microbial genomics. The real power of genomics is manifested through comparative genomics that can reveal strain specific characteristics, diversity within species and many other aspects. However, comparative genomics is a field not easily entered into by scientists with few computational skills. The CMG-biotools package is designed for microbiologists with limited knowledge of computational analysis and can be used to perform a number of analyses and comparisons of genomic data. The CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the system alongside any other operating system. Source codes for all programs are provided under GNU license, which makes it possible to transfer the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing the diversity within the class Negativicutes, represented by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures. This paper shows the strength and diverse use of the CMG-biotools system. The system can be installed on a vide range of host operating systems and utilizes as much of the host computer as desired. It allows the user to compare multiple genomes, from various sources using standardized data formats and intuitive visualizations of results. The examples presented here clearly shows that users with limited computational experience can perform complicated analysis without much training.

CMG-Biotools, a Free Workbench for Basic Comparative Microbial Genomics

PubMed Central

Vesth, Tammi; Lagesen, Karin; Acar, Öncel; Ussery, David

2013-01-01

Background Today, there are more than a hundred times as many sequenced prokaryotic genomes than were present in the year 2000. The economical sequencing of genomic DNA has facilitated a whole new approach to microbial genomics. The real power of genomics is manifested through comparative genomics that can reveal strain specific characteristics, diversity within species and many other aspects. However, comparative genomics is a field not easily entered into by scientists with few computational skills. The CMG-biotools package is designed for microbiologists with limited knowledge of computational analysis and can be used to perform a number of analyses and comparisons of genomic data. Results The CMG-biotools system presents a stand-alone interface for comparative microbial genomics. The package is a customized operating system, based on Xubuntu 10.10, available through the open source Ubuntu project. The system can be installed on a virtual computer, allowing the user to run the system alongside any other operating system. Source codes for all programs are provided under GNU license, which makes it possible to transfer the programs to other systems if so desired. We here demonstrate the package by comparing and analyzing the diversity within the class Negativicutes, represented by 31 genomes including 10 genera. The analyses include 16S rRNA phylogeny, basic DNA and codon statistics, proteome comparisons using BLAST and graphical analyses of DNA structures. Conclusion This paper shows the strength and diverse use of the CMG-biotools system. The system can be installed on a vide range of host operating systems and utilizes as much of the host computer as desired. It allows the user to compare multiple genomes, from various sources using standardized data formats and intuitive visualizations of results. The examples presented here clearly shows that users with limited computational experience can perform complicated analysis without much training. PMID:23577086

Comparative genomics approaches to understanding and manipulating plant metabolism.

PubMed

Bradbury, Louis M T; Niehaus, Tom D; Hanson, Andrew D

2013-04-01

Over 3000 genomes, including numerous plant genomes, are now sequenced. However, their annotation remains problematic as illustrated by the many conserved genes with no assigned function, vague annotations such as 'kinase', or even wrong ones. Around 40% of genes of unknown function that are conserved between plants and microbes are probably metabolic enzymes or transporters; finding functions for these genes is a major challenge. Comparative genomics has correctly predicted functions for many such genes by analyzing genomic context, and gene fusions, distributions and co-expression. Comparative genomics complements genetic and biochemical approaches to dissect metabolism, continues to increase in power and decrease in cost, and has a pivotal role in modeling and engineering by helping identify functions for all metabolic genes. Copyright © 2012 Elsevier Ltd. All rights reserved.

Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution

PubMed Central

Griffin, Darren K; Robertson, Lindsay B; Tempest, Helen G; Vignal, Alain; Fillon, Valérie; Crooijmans, Richard PMA; Groenen, Martien AM; Deryusheva, Svetlana; Gaginskaya, Elena; Carré, Wilfrid; Waddington, David; Talbot, Richard; Völker, Martin; Masabanda, Julio S; Burt, Dave W

2008-01-01

Background Comparative genomics is a powerful means of establishing inter-specific relationships between gene function/location and allows insight into genomic rearrangements, conservation and evolutionary phylogeny. The availability of the complete sequence of the chicken genome has initiated the development of detailed genomic information in other birds including turkey, an agriculturally important species where mapping has hitherto focused on linkage with limited physical information. No molecular study has yet examined conservation of avian microchromosomes, nor differences in copy number variants (CNVs) between birds. Results We present a detailed comparative cytogenetic map between chicken and turkey based on reciprocal chromosome painting and mapping of 338 chicken BACs to turkey metaphases. Two inter-chromosomal changes (both involving centromeres) and three pericentric inversions have been identified between chicken and turkey; and array CGH identified 16 inter-specific CNVs. Conclusion This is the first study to combine the modalities of zoo-FISH and array CGH between different avian species. The first insight into the conservation of microchromosomes, the first comparative cytogenetic map of any bird and the first appraisal of CNVs between birds is provided. Results suggest that avian genomes have remained relatively stable during evolution compared to mammalian equivalents. PMID:18410676

Simulation of halo particles with Simpsons

NASA Astrophysics Data System (ADS)

Machida, Shinji

2003-12-01

Recent code improvements and some simulation results of halo particles with Simpsons will be presented. We tried to identify resonance behavior of halo particles by looking at tune evolution of individual macro particle.

[TL, the new bacteriophage of Pseudomonas aeruginosa and its application for the search of halo-producing bacteriophages].

PubMed

Pleteneva, E A; Burkal'tseva, M V; Shaburova, O V; Krylov, S V; Pechnikova, E V; Sokolova, O S; Krylov, V N

2011-01-01

The properties of new virulent bacteriophage TL of Pseudomonas aeruginosa belonging to the family Podoviridae (genome size of 46 kb) were investigated. This bacteriophage is capable of lysogenizing the bacterial lawn in halo zones around negative colonies (NC) of other bacteriophages. TL forms large NC, that are hardly distinguishable on the lawn of P. aeruginisa PAO1. At the same time, on the lawns of some phage-resistant PAO1 mutants, as well as on those produced by a number of clinical isolates, TL forms more transparent NC. It is suggested that more effective growth of the bacteriophage TL NC is associated with the differences in outer lipopolysaccharide (LPS) layer of the cell walls of different bacterial strains, as well as of the bacteria inside and outside of the halos. This TL property was used to optimize selection of bacteriophages producing halos around NC on the lawn of P. aeruginosa PAO1. As a result, a group of bacteriophages differing in the patterns of interaction between their halos and TL bacteriophage, as well as in some characters was identified. Taking into consideration the importance of cell-surfaced structures of P. aeruginosa in manifestation of virulence and pathogenicity, possible utilization of specific phage enzymes, polysacchadide depolymerases, for more effective treatment of P. aeruginosa infections is discussed.

Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species.

PubMed

Hirao, Tomonori; Watanabe, Atsushi; Kurita, Manabu; Kondo, Teiji; Takata, Katsuhiko

2008-06-23

The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms. The C. japonica cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (trnI-CAU, trnQ-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the C. japonica cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as Cycas and Gingko, and additionally has completely lost its trnR-CCG, partially lost its trnT-GGU, and shows diversification of accD. The genomic structure of the C. japonica cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the Pinus thunbergii cp genome into that of C. japonica. In the C. japonica cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements. The observed differences in genomic structure between C. japonica and other land plants, including pines, strongly support the

Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont

PubMed Central

Lindsey, Amelia R. I.; Werren, John H.; Richards, Stephen; Stouthamer, Richard

2016-01-01

Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum. The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain. PMID:27194801

Comparative Genomics of a Parthenogenesis-Inducing Wolbachia Symbiont.

PubMed

Lindsey, Amelia R I; Werren, John H; Richards, Stephen; Stouthamer, Richard

2016-07-07

Wolbachia is an intracellular symbiont of invertebrates responsible for inducing a wide variety of phenotypes in its host. These host-Wolbachia relationships span the continuum from reproductive parasitism to obligate mutualism, and provide a unique system to study genomic changes associated with the evolution of symbiosis. We present the genome sequence from a parthenogenesis-inducing Wolbachia strain (wTpre) infecting the minute parasitoid wasp Trichogramma pretiosum The wTpre genome is the most complete parthenogenesis-inducing Wolbachia genome available to date. We used comparative genomics across 16 Wolbachia strains, representing five supergroups, to identify a core Wolbachia genome of 496 sets of orthologous genes. Only 14 of these sets are unique to Wolbachia when compared to other bacteria from the Rickettsiales. We show that the B supergroup of Wolbachia, of which wTpre is a member, contains a significantly higher number of ankyrin repeat-containing genes than other supergroups. In the wTpre genome, there is evidence for truncation of the protein coding sequences in 20% of ORFs, mostly as a result of frameshift mutations. The wTpre strain represents a conversion from cytoplasmic incompatibility to a parthenogenesis-inducing lifestyle, and is required for reproduction in the Trichogramma host it infects. We hypothesize that the large number of coding frame truncations has accompanied the change in reproductive mode of the wTpre strain. Copyright © 2016 Lindsey et al.

Neutron stars and white dwarfs in galactic halos

NASA Technical Reports Server (NTRS)

Ryu, Dongsu; Olive, Keith A.; Silk, Joseph

1989-01-01

The possibility that galactic halos are composed of stellar remnants such as neutron stars and white dwarfs is discussed. On the basis of a simple model for the evolution of galactic halos, researchers follow the history of halo matter, luminosity, and metal and helium abundances. They assume conventional yields for helium and the heavier elements. By comparing with the observational constraints, which may be considered as fairly conservative, it is found that, for an exponentially decreasing star formation rate (SFR) with e-folding time tau, only values between 6 x 10(8) less than similar to tau less than similar to 2 x 10(9) years are allowed together with a very limited range of masses for the initial mass function (IMF). Star formation is allowed for 2 solar mass less than similar to m less than similar to 8 solar mass if tau = 2 x 10(9) years, and for 4 solar mass less than similar to m less than similar to 6 solar mass if tau = 10(9) years. For tau = 6 x 10(8) years, the lower and upper mass limits merge to similar to 5 solar mass. Researchers conclude that, even though the possibility of neutron stars as halo matter may be ruled out, that of white dwarfs may still be a viable hypothesis, though with very stringent constraints on allowed parameters, that merits further consideration.

Self-consistent construction of virialized wave dark matter halos

NASA Astrophysics Data System (ADS)

Lin, Shan-Chang; Schive, Hsi-Yu; Wong, Shing-Kwong; Chiueh, Tzihong

2018-05-01

Wave dark matter (ψ DM ), which satisfies the Schrödinger-Poisson equation, has recently attracted substantial attention as a possible dark matter candidate. Numerical simulations have, in the past, provided a powerful tool to explore this new territory of possibility. Despite their successes in revealing several key features of ψ DM , further progress in simulations is limited, in that cosmological simulations so far can only address formation of halos below ˜2 ×1011 M⊙ and substantially more massive halos have become computationally very challenging to obtain. For this reason, the present work adopts a different approach in assessing massive halos by constructing wave-halo solutions directly from the wave distribution function. This approach bears certain similarities with the analytical construction of the particle-halo (cold dark matter model). Instead of many collisionless particles, one deals with one single wave that has many noninteracting eigenstates. The key ingredient in the wave-halo construction is the distribution function of the wave power, and we use several halos produced by structure formation simulations as templates to determine the wave distribution function. Among different models, we find the fermionic King model presents the best fits and we use it for our wave-halo construction. We have devised an iteration method for constructing the nonlinear halo and demonstrate its stability by three-dimensional simulations. A Milky Way-sized halo has also been constructed, and the inner halo is found to be flatter than the NFW profile. These wave-halos have small-scale interferences both in space and time producing time-dependent granules. While the spatial scale of granules varies little, the correlation time is found to increase with radius by 1 order of magnitude across the halo.

Jupiter's Ring Halo

NASA Technical Reports Server (NTRS)

1997-01-01

A mosaic of four images taken through the clear filter (610 nanometers) of the solid state imaging (CCD) system aboard NASA's Galileo spacecraft on November 8, 1996, at a resolution of approximately 46 kilometers (km) per picture element (pixel) along the rings; however, because the spacecraft was only about 0.5 degrees above the ring plane, the image is highly foreshortened in the vertical direction. The images were obtained when Galileo was in Jupiter's shadow peering back toward the Sun; the ring was approximately 2,300,000 kilometers (km) away. The arc on the far right of the image is produced by sunlight scattered by small particles comprising Jupiter's upper atmospheric haze. The ring also efficiently scatters light, indicating that much of its brightness is due to particles that are microns or less in diameter. Such small particles are believed to have human-scale lifetimes, i.e., very brief compared to the solar system's age.

Jupiter's ring system is composed of three parts -- a flat main ring, a lenticular halo interior to the main ring, and the gossamer ring, which lies exterior to the main ring. The near and far arms of Jupiter's main ring extend horizontally across the mosaic, joining together at the ring's ansa, on the far left side of the figure. The near arm of the ring appears to be abruptly truncated close to the planet, at the point where it passes into Jupiter's shadow.

A faint mist of particles can be seen above and below the main rings; this vertically extended, toroidal 'halo' is unusual in planetary rings, and is probably caused by electromagnetic forces which can push small grains out of the ring plane. Halo material is present across this entire image, implying that it reaches more than 27,000 km above the ring plane. Because of shadowing, the halo is not visible close to Jupiter in the lower right part of the mosaic. In order to accentuate faint features in the image, different brightnesses are shown through color, with the brightest

EDGAR: A software framework for the comparative analysis of prokaryotic genomes

PubMed Central

Blom, Jochen; Albaum, Stefan P; Doppmeier, Daniel; Pühler, Alfred; Vorhölter, Frank-Jörg; Zakrzewski, Martha; Goesmann, Alexander

2009-01-01

Background The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. Results To support these studies EDGAR – "Efficient Database framework for comparative Genome Analyses using BLAST score Ratios" – was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. Conclusion EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface , where the precomputed data sets can be browsed. PMID:19457249

How to get cool in the heat: comparing analytic models of hot, cold, and cooling gas in haloes and galaxies with EAGLE

NASA Astrophysics Data System (ADS)

Stevens, Adam R. H.; Lagos, Claudia del P.; Contreras, Sergio; Croton, Darren J.; Padilla, Nelson D.; Schaller, Matthieu; Schaye, Joop; Theuns, Tom

2017-05-01

We use the hydrodynamic, cosmological EAGLE simulations to investigate how the hot gas in haloes condenses to form and grow galaxies. We select haloes from the simulations that are actively cooling and study the temperature, distribution and metallicity of their hot, cold and transitioning 'cooling' gas, placing these in the context of semi-analytic models. Our selection criteria lead us to focus on Milky Way-like haloes. We find that the hot-gas density profiles of the haloes form a progressively stronger core over time, the nature of which can be captured by a β profile that has a simple dependence on redshift. In contrast, the hot gas that will cool over a time-step is broadly consistent with a singular isothermal sphere. We find that cooling gas carries a few times the specific angular momentum of the halo and is offset in spin direction from the rest of the hot gas. The gas loses ˜60 per cent of its specific angular momentum during the cooling process, generally remaining greater than that of the halo, and it precesses to become aligned with the cold gas already in the disc. We find tentative evidence that angular-momentum losses are slightly larger when gas cools on to dispersion-supported galaxies. We show that an exponential surface density profile for gas arriving on a disc remains a reasonable approximation, but a cusp containing ˜20 per cent of the mass is always present, and disc scale radii are larger than predicted by a vanilla Fall & Efstathiou model. These scale radii are still closely correlated with the halo spin parameter, for which we suggest an updated prescription for galaxy formation models.

Saccharomyces cerevisiae: gene annotation and genome variability, state of the art through comparative genomics.

PubMed

Louis, Ed

2011-01-01

In the early days of the yeast genome sequencing project, gene annotation was in its infancy and suffered the problem of many false positive annotations as well as missed genes. The lack of other sequences for comparison also prevented the annotation of conserved, functional sequences that were not coding. We are now in an era of comparative genomics where many closely related as well as more distantly related genomes are available for direct sequence and synteny comparisons allowing for more probable predictions of genes and other functional sequences due to conservation. We also have a plethora of functional genomics data which helps inform gene annotation for previously uncharacterised open reading frames (ORFs)/genes. For Saccharomyces cerevisiae this has resulted in a continuous updating of the gene and functional sequence annotations in the reference genome helping it retain its position as the best characterized eukaryotic organism's genome. A single reference genome for a species does not accurately describe the species and this is quite clear in the case of S. cerevisiae where the reference strain is not ideal for brewing or baking due to missing genes. Recent surveys of numerous isolates, from a variety of sources, using a variety of technologies have revealed a great deal of variation amongst isolates with genome sequence surveys providing information on novel genes, undetectable by other means. We now have a better understanding of the extant variation in S. cerevisiae as a species as well as some idea of how much we are missing from this understanding. As with gene annotation, comparative genomics enhances the discovery and description of genome variation and is providing us with the tools for understanding genome evolution, adaptation and selection, and underlying genetics of complex traits.

The tiger genome and comparative analysis with lion and snow leopard genomes.

PubMed

Cho, Yun Sung; Hu, Li; Hou, Haolong; Lee, Hang; Xu, Jiaohui; Kwon, Soowhan; Oh, Sukhun; Kim, Hak-Min; Jho, Sungwoong; Kim, Sangsoo; Shin, Young-Ah; Kim, Byung Chul; Kim, Hyunmin; Kim, Chang-Uk; Luo, Shu-Jin; Johnson, Warren E; Koepfli, Klaus-Peter; Schmidt-Küntzel, Anne; Turner, Jason A; Marker, Laurie; Harper, Cindy; Miller, Susan M; Jacobs, Wilhelm; Bertola, Laura D; Kim, Tae Hyung; Lee, Sunghoon; Zhou, Qian; Jung, Hyun-Ju; Xu, Xiao; Gadhvi, Priyvrat; Xu, Pengwei; Xiong, Yingqi; Luo, Yadan; Pan, Shengkai; Gou, Caiyun; Chu, Xiuhui; Zhang, Jilin; Liu, Sanyang; He, Jing; Chen, Ying; Yang, Linfeng; Yang, Yulan; He, Jiaju; Liu, Sha; Wang, Junyi; Kim, Chul Hong; Kwak, Hwanjong; Kim, Jong-Soo; Hwang, Seungwoo; Ko, Junsu; Kim, Chang-Bae; Kim, Sangtae; Bayarlkhagva, Damdin; Paek, Woon Kee; Kim, Seong-Jin; O'Brien, Stephen J; Wang, Jun; Bhak, Jong

2013-01-01

Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species.

The tiger genome and comparative analysis with lion and snow leopard genomes

PubMed Central

Cho, Yun Sung; Hu, Li; Hou, Haolong; Lee, Hang; Xu, Jiaohui; Kwon, Soowhan; Oh, Sukhun; Kim, Hak-Min; Jho, Sungwoong; Kim, Sangsoo; Shin, Young-Ah; Kim, Byung Chul; Kim, Hyunmin; Kim, Chang-uk; Luo, Shu-Jin; Johnson, Warren E.; Koepfli, Klaus-Peter; Schmidt-Küntzel, Anne; Turner, Jason A.; Marker, Laurie; Harper, Cindy; Miller, Susan M.; Jacobs, Wilhelm; Bertola, Laura D.; Kim, Tae Hyung; Lee, Sunghoon; Zhou, Qian; Jung, Hyun-Ju; Xu, Xiao; Gadhvi, Priyvrat; Xu, Pengwei; Xiong, Yingqi; Luo, Yadan; Pan, Shengkai; Gou, Caiyun; Chu, Xiuhui; Zhang, Jilin; Liu, Sanyang; He, Jing; Chen, Ying; Yang, Linfeng; Yang, Yulan; He, Jiaju; Liu, Sha; Wang, Junyi; Kim, Chul Hong; Kwak, Hwanjong; Kim, Jong-Soo; Hwang, Seungwoo; Ko, Junsu; Kim, Chang-Bae; Kim, Sangtae; Bayarlkhagva, Damdin; Paek, Woon Kee; Kim, Seong-Jin; O’Brien, Stephen J.; Wang, Jun; Bhak, Jong

2013-01-01

Tigers and their close relatives (Panthera) are some of the world’s most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats’ hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species. PMID:24045858

Modelling giant radio halos. Doctoral Thesis Award Lecture 2012

NASA Astrophysics Data System (ADS)

Donnert, J. M. F.

2013-06-01

We review models for giant radio halos in clusters of galaxies, with a focus on numerical and theoretical work. After summarising the most important observations of these objects, we present an introduction to the theoretical aspects of hadronic models. We compare these models with observations using simulations and find severe problems for hadronic models. We give a short introduction to reacceleration models and show results from the first simulation of CRe reacceleration in cluster mergers. We find that in-line with previous theoretical work, reacceleration models are able to elegantly explain main observables of giant radio halos.

Accurate mass and velocity functions of dark matter haloes

NASA Astrophysics Data System (ADS)

Comparat, Johan; Prada, Francisco; Yepes, Gustavo; Klypin, Anatoly

2017-08-01

N-body cosmological simulations are an essential tool to understand the observed distribution of galaxies. We use the MultiDark simulation suite, run with the Planck cosmological parameters, to revisit the mass and velocity functions. At redshift z = 0, the simulations cover four orders of magnitude in halo mass from ˜1011M⊙ with 8783 874 distinct haloes and 532 533 subhaloes. The total volume used is ˜515 Gpc3, more than eight times larger than in previous studies. We measure and model the halo mass function, its covariance matrix w.r.t halo mass and the large-scale halo bias. With the formalism of the excursion-set mass function, we explicit the tight interconnection between the covariance matrix, bias and halo mass function. We obtain a very accurate (<2 per cent level) model of the distinct halo mass function. We also model the subhalo mass function and its relation to the distinct halo mass function. The set of models obtained provides a complete and precise framework for the description of haloes in the concordance Planck cosmology. Finally, we provide precise analytical fits of the Vmax maximum velocity function up to redshift z < 2.3 to push for the development of halo occupation distribution using Vmax. The data and the analysis code are made publicly available in the Skies and Universes data base.

Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG.

PubMed

Uchiyama, Ikuo

2017-01-01

Comparative genomics is becoming an essential approach for identification of genes associated with a specific function or phenotype. Here, we introduce the microbial genome database for comparative analysis (MBGD), which is a comprehensive ortholog database among the microbial genomes available so far. MBGD contains several precomputed ortholog tables including the standard ortholog table covering the entire taxonomic range and taxon-specific ortholog tables for various major taxa. In addition, MBGD allows the users to create an ortholog table within any specified set of genomes through dynamic calculations. In particular, MBGD has a "My MBGD" mode where users can upload their original genome sequences and incorporate them into orthology analysis. The created ortholog table can serve as the basis for various comparative analyses. Here, we describe the use of MBGD and briefly explain how to utilize the orthology information during comparative genome analysis in combination with the stand-alone comparative genomics software RECOG, focusing on the application to comparison of closely related microbial genomes.

The MassiveBlack-II simulation: The evolution of haloes and galaxies to z ~ 0

DOE PAGES

Khandai, Nishikanta; Di Matteo, Tiziana; Croft, Rupert; ...

2015-04-24

We investigate the properties and clustering of halos, galaxies and blackholes to z = 0 in the high resolution hydrodynamical simulation MassiveBlack-II (MBII). MBII evolves a ΛCDM cosmology in a cubical comoving volume V box = (100Mpc/h)³. It is the highest resolution simulation of this size which includes a self-consistent model for star formation, black hole accretion and associated feedback. We provide a simulation browser web application which enables interactive search and tagging of the halos, subhalos and their properties and publicly release our galaxy catalogs to the scientific community. Our analysis of the halo mass function in MBII revealsmore » that baryons have strong effects with changes in the halo abundance of 20–35% below the knee of the mass function (M halo 10 13.2 M ⊙ h at z = 0) when compared to dark-matter-only simulations. We provide a fitting function for the halo MF out to redshift z = 11 and discuss its limitations.« less

The global dark halo structure of the Andromeda galaxy

NASA Astrophysics Data System (ADS)

Hayashi, Kohei; Chiba, Masashi

2014-01-01

We set new limits on the global shape of the dark halo in the Andromeda galaxy based on axisymmetric mass models constructed by Hayashi & Chiba (2012). This is motivated by the fact that CDM models predict non-spherical virialized dark halos, which reflect the process of mass assembly in the galactic scale. Based on the application of our models to latest kinematical data of globular clusters and dwarf spheroidal galaxies in the Andromeda halo, we find that the most plausible cases for Andromeda yield not a spherical but a prolate shape for its dark halo. We also find that the prolate dark halo is consistent with theoretical predictions in which the satellites are distributed anisotropically and preferentially located along major axes of their galactic host halos. It is a reflection of the intimate connection between galactic dark matter halos and the cosmic web.

Research Progresses of Halo Streams in the Solar Neighborhood

NASA Astrophysics Data System (ADS)

Xi-long, Liang; Jing-kun, Zhao; Yu-qin, Chen; Gang, Zhao

2018-01-01

The stellar streams originated from the Galactic halo may be detected when they pass by the solar neighborhood, and they still keep some information at their birth times. Thus, the investigation of halo streams in the solar neighborhood is very important for understanding the formation and evolution of our Galaxy. In this paper, the researches of halo streams in the solar neighborhood are briefly reviewed. We have introduced the methods how to detect the halo streams and identify their member stars, summarized the progresses in the observation of member stars of halo streams and in the study of their origins, introduced in detail how to analyze the origins of halo streams in the solar neighborhood by means of numerical simulation and chemical abundance, and finally discussed the prospects of the LAMOST and GAIA in the research of halo streams in the solar neighborhood.

Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes

PubMed Central

Doerr, Daniel; Chauve, Cedric

2017-01-01

Yersinia pestis is the causative agent of the bubonic plague, a disease responsible for several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible the sequencing of whole genomes of important human pathogens, including the ancient Y. pestis strains responsible for outbreaks of the bubonic plague in London in the 14th century and in Marseille in the 18th century, among others. However, aDNA sequencing data are still characterized by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging and often prevents a detailed study of genome rearrangements. It has recently been shown that comparative scaffolding approaches can improve the assembly of ancient Y. pestis genomes at a chromosome level. In the present work, we address the last step of genome assembly, the gap-filling stage. We describe an optimization-based method AGapEs (ancestral gap estimation) to fill in inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA reads. We show how this approach can be used to refine comparative scaffolding by selecting contig adjacencies supported by a mix of unassembled aDNA reads and comparative signal. We applied our method to two Y. pestis data sets from the London and Marseilles outbreaks, for which we obtained highly improved genome assemblies for both genomes, comprised of, respectively, five and six scaffolds with 95 % of the assemblies supported by ancient reads. We analysed the genome evolution between both ancient genomes in terms of genome rearrangements, and observed a high level of synteny conservation between these strains. PMID:29114402

A look into the inside of haloes: a characterization of the halo shape as a function of overdensity in the Planck cosmology

NASA Astrophysics Data System (ADS)

Despali, Giulia; Giocoli, Carlo; Bonamigo, Mario; Limousin, Marceau; Tormen, Giuseppe

2017-04-01

In this paper, we study the triaxial properties of dark matter haloes of a wide range of masses extracted from a set of cosmological N-body simulations. We measure the shape at different distances from the halo centre (characterized by different overdensity thresholds), both in three and in two dimensions. We discuss how halo triaxiality increases with mass, redshift and distance from the halo centre. We also examine how the orientations of the different ellipsoids are aligned with each other and what is the gradient in internal shapes for haloes with different virial configurations. Our findings highlight that the internal part of the halo retains memory of the violent formation process keeping the major axis oriented towards the preferential direction of the infalling material while the outer part becomes rounder due to continuous isotropic merging events. This effect is clearly evident in high-mass haloes - which formed more recently - while it is more blurred in low-mass haloes. We present simple distributions that may be used as priors for various mass reconstruction algorithms, operating in different wavelengths, in order to recover a more complex and realistic dark matter distribution of isolated and relaxed systems.

Halo correlations in nonlinear cosmic density fields

NASA Astrophysics Data System (ADS)

Bernardeau, F.; Schaeffer, R.

1999-09-01

The question we address in this paper is the determination of the correlation properties of the dark matter halos appearing in cosmic density fields once they underwent a strongly nonlinear evolution induced by gravitational dynamics. A series of previous works have given indications that kind of non-Gaussian features are induced by nonlinear evolution in term of the high-order correlation functions. Assuming such patterns for the matter field, i.e. that the high-order correlation functions behave as products of two-body correlation functions, we derive the correlation properties of the halos, that are assumed to represent the correlation properties of galaxies or clusters. The hierarchical pattern originally induced by gravity is shown to be conserved for the halos. The strength of their correlations at any order varies, however, but is found to depend only on their internal properties, namely on the parameter x~ m/r(3-gamma ) where m is the mass of the halo, r its size and gamma is the power law index of the two-body correlation function. This internal parameter is seen to be close to the depth of the internal potential well of virialized objects. We were able to derive the explicit form of the generating function of the moments of the halo counts probability distribution function. In particular we show explicitly that, generically, S_P(x)-> P(P-2) in the rare halo limit. Various illustrations of our general results are presented. As a function of the properties of the underlying matter field, we construct the count probabilities for halos and in particular discuss the halo void probability. We evaluate the dependence of the halo mass function on the environment: within clusters, hierarchical clustering implies the higher masses are favored. These properties solely arise from what is a natural bias (ie, naturally induced by gravity) between the observed objects and the unseen matter field, and how it manifests itself depending on which selection effects are

High Angular Momentum Halo Gas: A Feedback and Code-independent Prediction of LCDM

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

Stewart, Kyle R.; Maller, Ariyeh H.; Oñorbe, Jose

We investigate angular momentum acquisition in Milky Way-sized galaxies by comparing five high resolution zoom-in simulations, each implementing identical cosmological initial conditions but utilizing different hydrodynamic codes: Enzo, Art, Ramses, Arepo, and Gizmo-PSPH. Each code implements a distinct set of feedback and star formation prescriptions. We find that while many galaxy and halo properties vary between the different codes (and feedback prescriptions), there is qualitative agreement on the process of angular momentum acquisition in the galaxy’s halo. In all simulations, cold filamentary gas accretion to the halo results in ∼4 times more specific angular momentum in cold halo gas (more » λ {sub cold} ≳ 0.1) than in the dark matter halo. At z > 1, this inflow takes the form of inspiraling cold streams that are co-directional in the halo of the galaxy and are fueled, aligned, and kinematically connected to filamentary gas infall along the cosmic web. Due to the qualitative agreement among disparate simulations, we conclude that the buildup of high angular momentum halo gas and the presence of these inspiraling cold streams are robust predictions of Lambda Cold Dark Matter galaxy formation, though the detailed morphology of these streams is significantly less certain. A growing body of observational evidence suggests that this process is borne out in the real universe.« less

High Angular Momentum Halo Gas: A Feedback and Code-independent Prediction of LCDM

NASA Astrophysics Data System (ADS)

Stewart, Kyle R.; Maller, Ariyeh H.; Oñorbe, Jose; Bullock, James S.; Joung, M. Ryan; Devriendt, Julien; Ceverino, Daniel; Kereš, Dušan; Hopkins, Philip F.; Faucher-Giguère, Claude-André

2017-07-01

We investigate angular momentum acquisition in Milky Way-sized galaxies by comparing five high resolution zoom-in simulations, each implementing identical cosmological initial conditions but utilizing different hydrodynamic codes: Enzo, Art, Ramses, Arepo, and Gizmo-PSPH. Each code implements a distinct set of feedback and star formation prescriptions. We find that while many galaxy and halo properties vary between the different codes (and feedback prescriptions), there is qualitative agreement on the process of angular momentum acquisition in the galaxy’s halo. In all simulations, cold filamentary gas accretion to the halo results in ˜4 times more specific angular momentum in cold halo gas (λ cold ≳ 0.1) than in the dark matter halo. At z > 1, this inflow takes the form of inspiraling cold streams that are co-directional in the halo of the galaxy and are fueled, aligned, and kinematically connected to filamentary gas infall along the cosmic web. Due to the qualitative agreement among disparate simulations, we conclude that the buildup of high angular momentum halo gas and the presence of these inspiraling cold streams are robust predictions of Lambda Cold Dark Matter galaxy formation, though the detailed morphology of these streams is significantly less certain. A growing body of observational evidence suggests that this process is borne out in the real universe.

Gramene 2016: comparative plant genomics and pathway resources

USDA-ARS?s Scientific Manuscript database

Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the data...

Luminosity distance in Swiss-cheese cosmology with randomized voids and galaxy halos

NASA Astrophysics Data System (ADS)

Flanagan, Éanna É.; Kumar, Naresh; Wasserman, Ira

2013-08-01

We study the fluctuations in luminosity distance due to gravitational lensing produced both by galaxy halos and large-scale voids. Voids are represented via a “Swiss-cheese” model consisting of a ΛCDM Friedmann-Robertson-Walker background from which a number of randomly distributed, spherical regions of comoving radius 35 Mpc are removed. A fraction of the removed mass is then placed on the shells of the spheres, in the form of randomly located halos. The halos are assumed to be nonevolving and are modeled with Navarro-Frenk-White profiles of a fixed mass. The remaining mass is placed in the interior of the spheres, either smoothly distributed or as randomly located halos. We compute the distribution of magnitude shifts using a variant of the method of Holz and Wald [Phys. Rev. D 58, 063501 (1998)], which includes the effect of lensing shear. In the two models we consider, the standard deviation of this distribution is 0.065 and 0.072 magnitudes and the mean is -0.0010 and -0.0013 magnitudes, for voids of radius 35 Mpc and the sources at redshift 1.5, with the voids chosen so that 90% of the mass is on the shell today. The standard deviation due to voids and halos is a factor ˜3 larger than that due to 35 Mpc voids alone with a 1 Mpc shell thickness, which we studied in our previous work. We also study the effect of the existence of evacuated voids, by comparing to a model where all the halos are randomly distributed in the interior of the sphere with none on its surface. This does not significantly change the variance but does significantly change the demagnification tail. To a good approximation, the variance of the distribution depends only on the mean column density of halos (halo mass divided by its projected area), the concentration parameter of the halos, and the fraction of the mass density that is in the form of halos (as opposed to smoothly distributed); it is independent of how the halos are distributed in space. We derive an approximate analytic

IMG: the integrated microbial genomes database and comparative analysis system

PubMed Central

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

2012-01-01

The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. IMG's data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp). PMID:22194640

IMG: the Integrated Microbial Genomes database and comparative analysis system.

PubMed

Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos C

2012-01-01

The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. IMG's data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp).

Squeezing the halo bispectrum: a test of bias models

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

Dizgah, Azadeh Moradinezhad; Chan, Kwan Chuen; Noreña, Jorge

We study the halo-matter cross bispectrum in the presence of primordial non-Gaussianity of the local type. We restrict ourselves to the squeezed limit, for which the calculation are straightforward, and perform the measurements in the initial conditions of N-body simulations, to mitigate the contamination induced by nonlinear gravitational evolution. Interestingly, the halo-matter cross bispectrum is not trivial even in this simple limit as it is strongly sensitive to the scale-dependence of the quadratic and third-order halo bias. Therefore, it can be used to test biasing prescriptions. We consider three different prescription for halo clustering: excursion set peaks (ESP), local biasmore » and a model in which the halo bias parameters are explicitly derived from a peak-background split. In all cases, the model parameters are fully constrained with statistics other than the cross bispectrum. We measure the cross bispectrum involving one halo fluctuation field and two mass overdensity fields for various halo masses and collapse redshifts. We find that the ESP is in reasonably good agreement with the numerical data, while the other alternatives we consider fail in various cases. This suggests that the scale-dependence of halo bias also is a crucial ingredient to the squeezed limit of the halo bispectrum.« less

Protein attributes contribute to halo-stability, bioinformatics approach

PubMed Central

2011-01-01

Halophile proteins can tolerate high salt concentrations. Understanding halophilicity features is the first step toward engineering halostable crops. To this end, we examined protein features contributing to the halo-toleration of halophilic organisms. We compared more than 850 features for halophilic and non-halophilic proteins with various screening, clustering, decision tree, and generalized rule induction models to search for patterns that code for halo-toleration. Up to 251 protein attributes selected by various attribute weighting algorithms as important features contribute to halo-stability; from them 14 attributes selected by 90% of models and the count of hydrogen gained the highest value (1.0) in 70% of attribute weighting models, showing the importance of this attribute in feature selection modeling. The other attributes mostly were the frequencies of di-peptides. No changes were found in the numbers of groups when K-Means and TwoStep clustering modeling were performed on datasets with or without feature selection filtering. Although the depths of induced trees were not high, the accuracies of trees were higher than 94% and the frequency of hydrophobic residues pointed as the most important feature to build trees. The performance evaluation of decision tree models had the same values and the best correctness percentage recorded with the Exhaustive CHAID and CHAID models. We did not find any significant difference in the percent of correctness, performance evaluation, and mean correctness of various decision tree models with or without feature selection. For the first time, we analyzed the performance of different screening, clustering, and decision tree algorithms for discriminating halophilic and non-halophilic proteins and the results showed that amino acid composition can be used to discriminate between halo-tolerant and halo-sensitive proteins. PMID:21592393

MIPS PlantsDB: a database framework for comparative plant genome research.

PubMed

Nussbaumer, Thomas; Martis, Mihaela M; Roessner, Stephan K; Pfeifer, Matthias; Bader, Kai C; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

2013-01-01

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.

MIPS PlantsDB: a database framework for comparative plant genome research

PubMed Central

Nussbaumer, Thomas; Martis, Mihaela M.; Roessner, Stephan K.; Pfeifer, Matthias; Bader, Kai C.; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

2013-01-01

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB–plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834–D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB. PMID:23203886

HALOE test and evaluation software

NASA Technical Reports Server (NTRS)

Edmonds, W.; Natarajan, S.

1987-01-01

Computer programming, system development and analysis efforts during this contract were carried out in support of the Halogen Occultation Experiment (HALOE) at NASA/Langley. Support in the major areas of data acquisition and monitoring, data reduction and system development are described along with a brief explanation of the HALOE project. Documented listings of major software are located in the appendix.

Whole Genome Amplification of Labeled Viable Single Cells Suited for Array-Comparative Genomic Hybridization.

PubMed

Kroneis, Thomas; El-Heliebi, Amin

2015-01-01

Understanding details of a complex biological system makes it necessary to dismantle it down to its components. Immunostaining techniques allow identification of several distinct cell types thereby giving an inside view of intercellular heterogeneity. Often staining reveals that the most remarkable cells are the rarest. To further characterize the target cells on a molecular level, single cell techniques are necessary. Here, we describe the immunostaining, micromanipulation, and whole genome amplification of single cells for the purpose of genomic characterization. First, we exemplify the preparation of cell suspensions from cultured cells as well as the isolation of peripheral mononucleated cells from blood. The target cell population is then subjected to immunostaining. After cytocentrifugation target cells are isolated by micromanipulation and forwarded to whole genome amplification. For whole genome amplification, we use GenomePlex(®) technology allowing downstream genomic analysis such as array-comparative genomic hybridization.

Initial sequence and comparative analysis of the cat genome

PubMed Central

Pontius, Joan U.; Mullikin, James C.; Smith, Douglas R.; Lindblad-Toh, Kerstin; Gnerre, Sante; Clamp, Michele; Chang, Jean; Stephens, Robert; Neelam, Beena; Volfovsky, Natalia; Schäffer, Alejandro A.; Agarwala, Richa; Narfström, Kristina; Murphy, William J.; Giger, Urs; Roca, Alfred L.; Antunes, Agostinho; Menotti-Raymond, Marilyn; Yuhki, Naoya; Pecon-Slattery, Jill; Johnson, Warren E.; Bourque, Guillaume; Tesler, Glenn; O’Brien, Stephen J.

2007-01-01

The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing ∼65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence. PMID:17975172

Complete genome sequence and comparative genomics of the probiotic yeast Saccharomyces boulardii.

PubMed

Khatri, Indu; Tomar, Rajul; Ganesan, K; Prasad, G S; Subramanian, Srikrishna

2017-03-23

The probiotic yeast, Saccharomyces boulardii (Sb) is known to be effective against many gastrointestinal disorders and antibiotic-associated diarrhea. To understand molecular basis of probiotic-properties ascribed to Sb we determined the complete genomes of two strains of Sb i.e. Biocodex and unique28 and the draft genomes for three other Sb strains that are marketed as probiotics in India. We compared these genomes with 145 strains of S. cerevisiae (Sc) to understand genome-level similarities and differences between these yeasts. A distinctive feature of Sb from other Sc is absence of Ty elements Ty1, Ty3, Ty4 and associated LTR. However, we could identify complete Ty2 and Ty5 elements in Sb. The genes for hexose transporters HXT11 and HXT9, and asparagine-utilization are absent in all Sb strains. We find differences in repeat periods and copy numbers of repeats in flocculin genes that are likely related to the differential adhesion of Sb as compared to Sc. Core-proteome based taxonomy places Sb strains along with wine strains of Sc. We find the introgression of five genes from Z. bailii into the chromosome IV of Sb and wine strains of Sc. Intriguingly, genes involved in conferring known probiotic properties to Sb are conserved in most Sc strains.

Disc-halo interactions in ΛCDM

NASA Astrophysics Data System (ADS)

Bauer, Jacob S.; Widrow, Lawrence M.; Erkal, Denis

2018-05-01

We present a new method for embedding a stellar disc in a cosmological dark matter halo and provide a worked example from a Λ cold dark matter zoom-in simulation. The disc is inserted into the halo at a redshift z = 3 as a zero-mass rigid body. Its mass and size are then increased adiabatically while its position, velocity, and orientation are determined from rigid-body dynamics. At z = 1, the rigid disc (RD) is replaced by an N-body disc whose particles sample a three-integral distribution function (DF). The simulation then proceeds to z = 0 with live disc (LD) and halo particles. By comparison, other methods assume one or more of the following: the centre of the RD during the growth phase is pinned to the minimum of the halo potential, the orientation of the RD is fixed, or the live N-body disc is constructed from a two rather than three-integral DF. In general, the presence of a disc makes the halo rounder, more centrally concentrated, and smoother, especially in the innermost regions. We find that methods in which the disc is pinned to the minimum of the halo potential tend to overestimate the amount of adiabatic contraction. Additionally, the effect of the disc on the subhalo distribution appears to be rather insensitive to the disc insertion method. The LD in our simulation develops a bar that is consistent with the bars seen in late-type spiral galaxies. In addition, particles from the disc are launched or `kicked up' to high galactic latitudes.

Oxygen abundances in halo giants. I - Giants in the very metal-poor globular clusters M92 and M15 and the metal-poor halo field

NASA Astrophysics Data System (ADS)

Sneden, Christopher; Kraft, Robert P.; Prosser, Charles F.; Langer, G. E.

1991-12-01

Oxygen, iron, vanadium, and scandium abundances are derived for very metal-poor giants in the globular clusters M92 and M15, and giants of comparable metallicity in the local halo field. The forbidden O I line dublet (6300, 6363) and nearby metallic lines in spectra are analyzed using line analysis and spectral synthesis codes. The Fe/H abundance for M92 is estimated at -2.25 +/-0.02 based on nine giants with a range of 500 K in effective temperature. No evidence for star-to-star variations in the Fe/H abundance was found. O-rich and O-poor stars appear intermixed in the H-R diagram. O - N nuclear synthesis and mixing to the surface are proposed as the best explanation for the low-oxygen giants. The nitrogen abundances obtained earlier for nine of the ten halo field giants in this sample are incompatible with the very large nitrogen abundances expected of the O/Fe abundance of about + 1.2 in halo field subdwarfs, as found by Abia and Rebolo (1989), and not more than 0.6 in halo giants, as found in this and other studies.

Genome-Wide Comparative Gene Family Classification

PubMed Central

Frech, Christian; Chen, Nansheng

2010-01-01

Correct classification of genes into gene families is important for understanding gene function and evolution. Although gene families of many species have been resolved both computationally and experimentally with high accuracy, gene family classification in most newly sequenced genomes has not been done with the same high standard. This project has been designed to develop a strategy to effectively and accurately classify gene families across genomes. We first examine and compare the performance of computer programs developed for automated gene family classification. We demonstrate that some programs, including the hierarchical average-linkage clustering algorithm MC-UPGMA and the popular Markov clustering algorithm TRIBE-MCL, can reconstruct manual curation of gene families accurately. However, their performance is highly sensitive to parameter setting, i.e. different gene families require different program parameters for correct resolution. To circumvent the problem of parameterization, we have developed a comparative strategy for gene family classification. This strategy takes advantage of existing curated gene families of reference species to find suitable parameters for classifying genes in related genomes. To demonstrate the effectiveness of this novel strategy, we use TRIBE-MCL to classify chemosensory and ABC transporter gene families in C. elegans and its four sister species. We conclude that fully automated programs can establish biologically accurate gene families if parameterized accordingly. Comparative gene family classification finds optimal parameters automatically, thus allowing rapid insights into gene families of newly sequenced species. PMID:20976221

Halo-free phase contrast microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Nguyen, Tan H.; Kandel, Mikhail E.; Shakir, Haadi M.; Best, Catherine; Do, Minh N.; Popescu, Gabriel

2017-02-01

The phase contrast (PC) method is one of the most impactful developments in the four-century long history of microscopy. It allows for intrinsic, nondestructive contrast of transparent specimens, such as live cells. However, PC is plagued by the halo artifact, a result of insufficient spatial coherence in the illumination field, which limits its applicability. We present a new approach for retrieving halo-free phase contrast microscopy (hfPC) images by upgrading the conventional PC microscope with an external interferometric module, which generates sufficient data for reversing the halo artifact. Measuring four independent intensity images, our approach first measures haloed phase maps of the sample. We solve for the halo-free sample transmission function by using a physical model of the image formation under partial spatial coherence. Using this halo-free sample transmission, we can numerically generate artifact-free PC images. Furthermore, this transmission can be further used to obtain quantitative information about the sample, e.g., the thickness with known refractive indices, dry mass of live cells during their cycles. We tested our hfPC method on various control samples, e.g., beads, pillars and validated its potential for biological investigation by imaging live HeLa cells, red blood cells, and neurons.

The Structure of Dark Matter Halos in Dwarf Galaxies

NASA Astrophysics Data System (ADS)

Burkert, A.

1995-07-01

Recent observations indicate that dark matter halos have flat central density profiles. Cosmological simulations with nonbaryonic dark matter, however, predict self-similar halos with central density cusps. This contradiction has lead to the conclusion that dark matter must be baryonic. Here it is shown that the dark matter halos of dwarf spiral galaxies represent a one-parameter family with self-similar density profiles. The observed global halo parameters are coupled with each other through simple scaling relations which can be explained by the standard cold dark matter model if one assumes that all the halos formed from density fluctuations with the same primordial amplitude. We find that the finite central halo densities correlate with the other global parameters. This result rules out scenarios where the flat halo cores formed subsequently through violent dynamical processes in the baryonic component. These cores instead provide important information on the origin and nature of dark matter in dwarf galaxies.

The growth and structure of dark matter haloes

NASA Astrophysics Data System (ADS)

Zhao, D. H.; Mo, H. J.; Jing, Y. P.; Börner, G.

2003-02-01

In this paper, we analyse in detail the mass-accretion histories and structural properties of dark haloes in high-resolution N-body simulations. We model the density distribution in individual haloes using the Navarro-Frenk-White (NFW) profile. For a given halo, there is a tight correlation between its inner-scale radius rs and the mass within it, Ms, for all its main progenitors. Using this correlation, one can predict quite well the structural properties of a dark halo at any time in its history from its mass-accretion history, implying that the structure properties and the mass-accretion history are closely correlated. The predicted growing rate of concentration c with time tends to increase with decreasing mass-accretion rate. The build-up of dark haloes in cold dark matter (CDM) models generally consists of an early phase of fast accretion (where the halo mass Mh increases with time much faster than the expansion rate of the Universe) and a late phase of slow accretion (where Mh increases with time approximately as the expansion rate). These two phases are separated at a time when c~ 4 and the typical binding energy of the halo is approximately equal to that of a singular isothermal sphere with the same circular velocity. Haloes in the two accretion phases show systematically different properties, for example, the circular velocity vh increases rapidly with time in the fast accretion phase but remains almost constant in the slow accretion phase, the inner properties of a halo, such as rs and Ms increase rapidly with time in the fast accretion phase but change only slowly in the slow accretion phase, the inner circular velocity vs is approximately equal to vh in the fast accretion phase but is larger in the slow accretion phase. The potential well associated with a halo is built up mainly in the fast accretion phase, while a large amount of mass can be accreted in the slow accretion phase without changing the potential well significantly. We discuss our results

Halos--a problem for all myopes? A comparison between spectacles, contact lenses, and photorefractive keratectomy.

PubMed

Lohmann, C P; Fitzke, F W; O'Brart, D; Muir, M K; Marshall, J

1993-01-01

After photorefractive keratectomy (PRK) using excimer lasers (193 nm) many patients report the presence of halos around light sources at night. However, halos are not unique to PRK patients, as they are a common observation in myopic contact lens wearers. We present an objective measurement of the halos using a computerized technique. The patient fixated on a red cross within a white circle in the center of a video monitor which served as the halo source. The screen surrounding the circle was not illuminated. The operator controlled the movement of the white spot and moved the spot toward the halo source until the subject indicated when the cursor was at the outer parameter of the halo. Measurements were made at 30 degree intervals around the halo source and expressed as square degrees. The study found that spectacles, soft contact lenses, and excimer laser surgery were superior to hard contact lenses in terms of the size of the halo. A mean value of 2.51 square degrees was obtained for spectacles wearers compared with 3.18 square degrees for soft contact lenses, 3.14 square degrees for excimer laser patients with 4-millimeter ablation zone, 2.76 square degrees for excimer laser patients with a 5-millimeter ablation zone, and 89.5 square degrees for hard contact lenses. It appears that this device is very useful for measuring the halo size after excimer laser PRK. We concluded that halos were not a problem for our patients after excimer laser photorefractive keratectomy.

The Impact of Starbursts on the Gaseous Halos of Galaxies

NASA Astrophysics Data System (ADS)

Heckman, Timothy

2009-07-01

Perhaps the most important {yet uncertain} aspects of galaxy evolution are the processes by which galaxies accrete gas and by which the resulting star formation and black hole growth affects this accreting gas. It is believed that both the form of the accretion and the nature of the feedback change as a function of the galaxy mass. At low mass the gas comes in cold and the feedback is provided by massive stars. At high mass, the gas comes in hot, and the feedback is from an AGN. The changeover occurs near the mass where the galaxy population transitions from star-forming galaxies to red and dead ones. The population of red and dead galaxies is building with cosmic time, and it is believed that feedback plays an imporant role in this process: shutting down star formation by heating and/or expelling the reservoir of cold halo gas. To investigate these ideas, we propose to use COS far-UV spectra of background QSOs to measure the properties of the halo gas in a sample of galaxies near the transition mass that have undergone starbursts within the past 100 Myr to 1 Gyr. The galactic wind associated with the starburst is predicted to have affected the properties of the gaseous halo. To test this, we will compare the properties of the halos of the post-starburst galaxies to those of a control sample of galaxies matched in mass and QSO impact parameter. Do the halos of the post-starburst galaxies show a higher incidence rate of Ly-Alpha and metal absorption-lines? Are the kinematics of the halo gas more disturbed in the post-starbursts? Has the wind affected the ionization state and/or the metallicity of the halo? These data will provide fresh new insights into the role of feedback from massive stars on the evolution of galaxies, and may also offer clues about the properties of the QSO metal absorption-line systems at high-redshift.

N-body dark matter haloes with simple hierarchical histories

NASA Astrophysics Data System (ADS)

Jiang, Lilian; Helly, John C.; Cole, Shaun; Frenk, Carlos S.

2014-05-01

We present a new algorithm which groups the subhaloes found in cosmological N-body simulations by structure finders such as SUBFIND into dark matter haloes whose formation histories are strictly hierarchical. One advantage of these `Dhaloes' over the commonly used friends-of-friends (FoF) haloes is that they retain their individual identity in the cases when FoF haloes are artificially merged by tenuous bridges of particles or by an overlap of their outer diffuse haloes. Dhaloes are thus well suited for modelling galaxy formation and their merger trees form the basis of the Durham semi-analytic galaxy formation model, GALFORM. Applying the Dhalo construction to the Λ cold dark matter Millennium II Simulation, we find that approximately 90 per cent of Dhaloes have a one-to-one, bijective match with a corresponding FoF halo. The remaining 10 per cent are typically secondary components of large FoF haloes. Although the mass functions of both types of haloes are similar, the mass of Dhaloes correlates much more tightly with the virial mass, M200, than FoF haloes. Approximately 80 per cent of FoF and bijective and non-bijective Dhaloes are relaxed according to standard criteria. For these relaxed haloes, all three types have similar concentration-M200 relations and, at fixed mass, the concentration distributions are described accurately by log-normal distributions.

The Origin of the Milky Way's Halo Age Distribution

NASA Astrophysics Data System (ADS)

Carollo, Daniela; Tissera, Patricia B.; Beers, Timothy C.; Gudin, Dmitrii; Gibson, Brad K.; Freeman, Ken C.; Monachesi, Antonela

2018-05-01

We present an analysis of the radial age gradients for the stellar halos of five Milky Way (MW) mass-sized systems simulated as part of the Aquarius Project. The halos show a diversity of age trends, reflecting their different assembly histories. Four of the simulated halos possess clear negative age gradients, ranging from approximately ‑7 to ‑19 Myr kpc‑1, shallower than those determined by recent observational studies of the Milky Way’s stellar halo. However, when restricting the analysis to the accreted component alone, all of the stellar halos exhibit a steeper negative age gradient with values ranging from ‑8 to ‑32 Myr kpc‑1, closer to those observed in the Galaxy. Two of the accretion-dominated simulated halos show a large concentration of old stars in the center, in agreement with the Ancient Chronographic Sphere reported observationally. The stellar halo that best reproduces the current observed characteristics of the age distributions of the Galaxy is that formed principally by the accretion of small satellite galaxies. Our findings suggest that the hierarchical clustering scenario can reproduce the MW’s halo age distribution if the stellar halo was assembled from accretion and the disruption of satellite galaxies with dynamical masses less than ∼109.5 M ⊙, and a minimal in situ contribution.

PLAZA 3.0: an access point for plant comparative genomics

PubMed Central

Proost, Sebastian; Van Bel, Michiel; Vaneechoutte, Dries; Van de Peer, Yves; Inzé, Dirk; Mueller-Roeber, Bernd; Vandepoele, Klaas

2015-01-01

Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms. PMID:25324309

Comparative Genomics of Carp Herpesviruses

PubMed Central

Kurobe, Tomofumi; Gatherer, Derek; Cunningham, Charles; Korf, Ian; Fukuda, Hideo; Hedrick, Ronald P.; Waltzek, Thomas B.

2013-01-01

Three alloherpesviruses are known to cause disease in cyprinid fish: cyprinid herpesviruses 1 and 3 (CyHV1 and CyHV3) in common carp and koi and cyprinid herpesvirus 2 (CyHV2) in goldfish. We have determined the genome sequences of CyHV1 and CyHV2 and compared them with the published CyHV3 sequence. The CyHV1 and CyHV2 genomes are 291,144 and 290,304 bp, respectively, in size, and thus the CyHV3 genome, at 295,146 bp, remains the largest recorded among the herpesviruses. Each of the three genomes consists of a unique region flanked at each terminus by a sizeable direct repeat. The CyHV1, CyHV2, and CyHV3 genomes are predicted to contain 137, 150, and 155 unique, functional protein-coding genes, respectively, of which six, four, and eight, respectively, are duplicated in the terminal repeat. The three viruses share 120 orthologous genes in a largely colinear arrangement, of which up to 55 are also conserved in the other member of the genus Cyprinivirus, anguillid herpesvirus 1. Twelve genes are conserved convincingly in all sequenced alloherpesviruses, and two others are conserved marginally. The reference CyHV3 strain has been reported to contain five fragmented genes that are presumably nonfunctional. The CyHV2 strain has two fragmented genes, and the CyHV1 strain has none. CyHV1, CyHV2, and CyHV3 have five, six, and five families of paralogous genes, respectively. One family unique to CyHV1 is related to cellular JUNB, which encodes a transcription factor involved in oncogenesis. To our knowledge, this is the first time that JUNB-related sequences have been reported in a herpesvirus. PMID:23269803

Comparative genomics of biotechnologically important yeasts

USDA-ARS?s Scientific Manuscript database

Ascomycete yeasts are metabolically diverse, with great potential for biotechnology. Here, we report the comparative genome analysis of 29 taxonomically and biotechnologically important yeasts, including 16 newly sequenced. We identify a genetic code change, CUG-Ala, in Pachysolen tannophilus in the...

Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge

PubMed Central

Gusev, Oleg; Suetsugu, Yoshitaka; Cornette, Richard; Kawashima, Takeshi; Logacheva, Maria D.; Kondrashov, Alexey S.; Penin, Aleksey A.; Hatanaka, Rie; Kikuta, Shingo; Shimura, Sachiko; Kanamori, Hiroyuki; Katayose, Yuichi; Matsumoto, Takashi; Shagimardanova, Elena; Alexeev, Dmitry; Govorun, Vadim; Wisecaver, Jennifer; Mikheyev, Alexander; Koyanagi, Ryo; Fujie, Manabu; Nishiyama, Tomoaki; Shigenobu, Shuji; Shibata, Tomoko F.; Golygina, Veronika; Hasebe, Mitsuyasu; Okuda, Takashi; Satoh, Nori; Kikawada, Takahiro

2014-01-01

Anhydrobiosis represents an extreme example of tolerance adaptation to water loss, where an organism can survive in an ametabolic state until water returns. Here we report the first comparative analysis examining the genomic background of extreme desiccation tolerance, which is exclusively found in larvae of the only anhydrobiotic insect, Polypedilum vanderplanki. We compare the genomes of P. vanderplanki and a congeneric desiccation-sensitive midge P. nubifer. We determine that the genome of the anhydrobiotic species specifically contains clusters of multi-copy genes with products that act as molecular shields. In addition, the genome possesses several groups of genes with high similarity to known protective proteins. However, these genes are located in distinct paralogous clusters in the genome apart from the classical orthologues of the corresponding genes shared by both chironomids and other insects. The transcripts of these clustered paralogues contribute to a large majority of the mRNA pool in the desiccating larvae and most likely define successful anhydrobiosis. Comparison of expression patterns of orthologues between two chironomid species provides evidence for the existence of desiccation-specific gene expression systems in P. vanderplanki. PMID:25216354

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies.

PubMed

Thakur, Shalabh; Guttman, David S

2016-06-30

Comparative analysis of whole genome sequence data from closely related prokaryotic species or strains is becoming an increasingly important and accessible approach for addressing both fundamental and applied biological questions. While there are number of excellent tools developed for performing this task, most scale poorly when faced with hundreds of genome sequences, and many require extensive manual curation. We have developed a de-novo genome analysis pipeline (DeNoGAP) for the automated, iterative and high-throughput analysis of data from comparative genomics projects involving hundreds of whole genome sequences. The pipeline is designed to perform reference-assisted and de novo gene prediction, homolog protein family assignment, ortholog prediction, functional annotation, and pan-genome analysis using a range of proven tools and databases. While most existing methods scale quadratically with the number of genomes since they rely on pairwise comparisons among predicted protein sequences, DeNoGAP scales linearly since the homology assignment is based on iteratively refined hidden Markov models. This iterative clustering strategy enables DeNoGAP to handle a very large number of genomes using minimal computational resources. Moreover, the modular structure of the pipeline permits easy updates as new analysis programs become available. DeNoGAP integrates bioinformatics tools and databases for comparative analysis of a large number of genomes. The pipeline offers tools and algorithms for annotation and analysis of completed and draft genome sequences. The pipeline is developed using Perl, BioPerl and SQLite on Ubuntu Linux version 12.04 LTS. Currently, the software package accompanies script for automated installation of necessary external programs on Ubuntu Linux; however, the pipeline should be also compatible with other Linux and Unix systems after necessary external programs are installed. DeNoGAP is freely available at https://sourceforge.net/projects/denogap/ .

CFGP: a web-based, comparative fungal genomics platform.

PubMed

Park, Jongsun; Park, Bongsoo; Jung, Kyongyong; Jang, Suwang; Yu, Kwangyul; Choi, Jaeyoung; Kong, Sunghyung; Park, Jaejin; Kim, Seryun; Kim, Hyojeong; Kim, Soonok; Kim, Jihyun F; Blair, Jaime E; Lee, Kwangwon; Kang, Seogchan; Lee, Yong-Hwan

2008-01-01

Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the 'fill-in-the-form-and-press-SUBMIT' user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI.

CFGP: a web-based, comparative fungal genomics platform

PubMed Central

Park, Jongsun; Park, Bongsoo; Jung, Kyongyong; Jang, Suwang; Yu, Kwangyul; Choi, Jaeyoung; Kong, Sunghyung; Park, Jaejin; Kim, Seryun; Kim, Hyojeong; Kim, Soonok; Kim, Jihyun F.; Blair, Jaime E.; Lee, Kwangwon; Kang, Seogchan; Lee, Yong-Hwan

2008-01-01

Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the ‘fill-in-the-form-and-press-SUBMIT’ user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI. PMID:17947331

Isobar analog states (IAS), double isobar analog states (DIAS), configuration states (CS), and double configuration states (DCS) in halo nuclei. Halo isomers

NASA Astrophysics Data System (ADS)

Izosimov, I. N.

2015-10-01

It has been shown that IAS, DIAS, CS, and DCS can simultaneously have n-n, n-p, and p-p halo components in their wave functions. Differences in halo structure of the excited and ground states can result in the formation of isomers (halo-isomers). Both the Borromean and tango halo types can be observed for n-p configurations of atomic nuclei. The structure of the ground and excited states with different isospin quantum number in halo like nuclei is discussed. B(Mλ) and B(Eλ) for γ-transitions in 6,7,8Li, 8,9,10Be, 8,10,11B, 10,11,12,13,14C, 13,14,15,16,17N, 15,16,17,19O, and 17F are analyzed. Special attention is given to nuclei whose ground state does not exhibit halo structure but the excited state may have one.

Conserved actions, maximum entropy and dark matter haloes

NASA Astrophysics Data System (ADS)

Pontzen, Andrew; Governato, Fabio

2013-03-01

We use maximum entropy arguments to derive the phase-space distribution of a virialized dark matter halo. Our distribution function gives an improved representation of the end product of violent relaxation. This is achieved by incorporating physically motivated dynamical constraints (specifically on orbital actions) which prevent arbitrary redistribution of energy. We compare the predictions with three high-resolution dark matter simulations of widely varying mass. The numerical distribution function is accurately predicted by our argument, producing an excellent match for the vast majority of particles. The remaining particles constitute the central cusp of the halo (≲4 per cent of the dark matter). They can be accounted for within the presented framework once the short dynamical time-scales of the centre are taken into account.

Mycobacterial species as case-study of comparative genome analysis.

PubMed

Zakham, F; Belayachi, L; Ussery, D; Akrim, M; Benjouad, A; El Aouad, R; Ennaji, M M

2011-02-08

The genus Mycobacterium represents more than 120 species including important pathogens of human and cause major public health problems and illnesses. Further, with more than 100 genome sequences from this genus, comparative genome analysis can provide new insights for better understanding the evolutionary events of these species and improving drugs, vaccines, and diagnostics tools for controlling Mycobacterial diseases. In this present study we aim to outline a comparative genome analysis of fourteen Mycobacterial genomes: M. avium subsp. paratuberculosis K—10, M. bovis AF2122/97, M. bovis BCG str. Pasteur 1173P2, M. leprae Br4923, M. marinum M, M. sp. KMS, M. sp. MCS, M. tuberculosis CDC1551, M. tuberculosis F11, M. tuberculosis H37Ra, M. tuberculosis H37Rv, M. tuberculosis KZN 1435 , M. ulcerans Agy99,and M. vanbaalenii PYR—1, For this purpose a comparison has been done based on their length of genomes, GC content, number of genes in different data bases (Genbank, Refseq, and Prodigal). The BLAST matrix of these genomes has been figured to give a lot of information about the similarity between species in a simple scheme. As a result of multiple genome analysis, the pan and core genome have been defined for twelve Mycobacterial species. We have also introduced the genome atlas of the reference strain M. tuberculosis H37Rv which can give a good overview of this genome. And for examining the phylogenetic relationships among these bacteria, a phylogenic tree has been constructed from 16S rRNA gene for tuberculosis and non tuberculosis Mycobacteria to understand the evolutionary events of these species.

An improved catalog of halo wide binary candidates

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

Allen, Christine; Monroy-Rodríguez, Miguel A., E-mail: chris@astro.unam.mx

2014-08-01

We present an improved catalog of halo wide binaries compiled from an extensive literature search. Most of our binaries stem from the common proper motion binary catalogs by Allen et al. and Chanamé and Gould, but we have also included binaries from the lists of Ryan and Zapatero-Osorio and Martín. All binaries were carefully checked and their distances and systemic radial velocities are included when available. Probable membership to the halo population was tested by means of reduced proper motion diagrams for 251 candidate halo binaries. After eliminating obvious disk binaries, we ended up with 211 probable halo binaries, 150more » of which have radial velocities available. We compute galactic orbits for these 150 binaries and calculate the time they spend within the galactic disk. Considering the full sample of 251 candidate halo binaries as well as several subsamples, we find that the distribution of angular separations (or expected major semiaxes) follows a power law f(a) ∼ a {sup –1} (Oepik's relation) up to different limits. For the 50 most disk-like binaries, those that spend their entire lives within z = ±500 pc, this limit is found to be 19,000 AU (0.09 pc), while for the 50 most halo-like binaries, those that spend on average only 18% of their lives within z = ±500 pc, the limit is 63,000 AU (0.31 pc). In a companion paper, we employ this catalog to establish limits on the masses of the halo massive perturbers (massive compact halo objects).« less

BactoGeNIE: A large-scale comparative genome visualization for big displays

DOE PAGES

Aurisano, Jillian; Reda, Khairi; Johnson, Andrew; ...

2015-08-13

The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE throughmore » a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. In conclusion, BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.« less

BactoGeNIE: a large-scale comparative genome visualization for big displays

PubMed Central

2015-01-01

Background The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. Results In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE through a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. Conclusions BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics. PMID:26329021

BactoGeNIE: A large-scale comparative genome visualization for big displays

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

Aurisano, Jillian; Reda, Khairi; Johnson, Andrew

The volume of complete bacterial genome sequence data available to comparative genomics researchers is rapidly increasing. However, visualizations in comparative genomics--which aim to enable analysis tasks across collections of genomes--suffer from visual scalability issues. While large, multi-tiled and high-resolution displays have the potential to address scalability issues, new approaches are needed to take advantage of such environments, in order to enable the effective visual analysis of large genomics datasets. In this paper, we present Bacterial Gene Neighborhood Investigation Environment, or BactoGeNIE, a novel and visually scalable design for comparative gene neighborhood analysis on large display environments. We evaluate BactoGeNIE throughmore » a case study on close to 700 draft Escherichia coli genomes, and present lessons learned from our design process. In conclusion, BactoGeNIE accommodates comparative tasks over substantially larger collections of neighborhoods than existing tools and explicitly addresses visual scalability. Given current trends in data generation, scalable designs of this type may inform visualization design for large-scale comparative research problems in genomics.« less

The Phase-space Density Distribution of Dark Matter Halos

NASA Astrophysics Data System (ADS)

Williams, Liliya L. R.; Austin, Crystal; Barnes, Eric; Babul, Arif; Dalcanton, Julianne

2004-12-01

High resolution N-body simulations have all but converged on a common empirical form for the shape of the density profiles of halos, but the full understanding of the underlying physics of halo formation has eluded them so far. We investigate the formation and structure of dark matter halos using analytical and semi-analytical techniques. Our halos are formed via an extended secondary infall model (ESIM); they contain secondary perturbations and hence random tangential and ra- dial motions which affect the halo’s evolution at it undergoes shell-crossing and virialization. Even though the density profiles of NFW and ESIM halos are different their phase-space density distributions are the same: ρ σ3 ∝ r α , with α 1 875 over 3 decades in radius. We use two approaches to try to explain this “universal” slope: (1) The Jeans equation analysis yields many insights, however, does not answer why α 1 875. (2) The secondary infall model of the 1960’s £ ¤ and 1970’s, augmented by “thermal motions” of particles does predict that halos should have α 1 875. However, this relies on assumptions of spherical symmetry and slow accretion. While £ ¤ for ESIM halos these assumptions are justified, they most certainly break down for simulated halos which forms hierarchically. We speculate that our argument may apply to an “on-average” formation scenario of halos within merger-driven numerical simulations, and thereby explain why α 1 875 for NFW halos. Thus, ρ σ3 ∝ r 1 875 may be a generic feature of violent relaxation.

Bimodal Formation Time Distribution for Infall Dark Matter Halos

NASA Astrophysics Data System (ADS)

Shi, Jingjing; Wang, Huiyuan; Mo, H. J.; Xie, Lizhi; Wang, Xiaoyu; Lapi, Andrea; Sheth, Ravi K.

2018-04-01

We use a 200 {h}-1 {Mpc} a-side N-body simulation to study the mass accretion history (MAH) of dark matter halos to be accreted by larger halos, which we call infall halos. We define a quantity {a}nf}\\equiv (1+{z}{{f}})/(1+{z}peak}) to characterize the MAH of infall halos, where {z}peak} and {z}{{f}} are the accretion and formation redshifts, respectively. We find that, at given {z}peak}, their MAH is bimodal. Infall halos are dominated by a young population at high redshift and by an old population at low redshift. For the young population, the {a}nf} distribution is narrow and peaks at about 1.2, independent of {z}peak}, while for the old population, the peak position and width of the {a}nf} distribution both increase with decreasing {z}peak} and are both larger than those of the young population. This bimodal distribution is found to be closely connected to the two phases in the MAHs of halos. While members of the young population are still in the fast accretion phase at z peak, those of the old population have already entered the slow accretion phase at {z}peak}. This bimodal distribution is not found for the whole halo population, nor is it seen in halo merger trees generated with the extended Press–Schechter formalism. The infall halo population at {z}peak} are, on average, younger than the whole halo population of similar masses identified at the same redshift. We discuss the implications of our findings in connection to the bimodal color distribution of observed galaxies and to the link between central and satellite galaxies.

What sets the central structure of dark matter haloes?

NASA Astrophysics Data System (ADS)

Ogiya, Go; Hahn, Oliver

2018-02-01

Dark matter (DM) haloes forming near the thermal cut-off scale of the density perturbations are unique, since they are the smallest objects and form through monolithic gravitational collapse, while larger haloes contrastingly have experienced mergers. While standard cold dark matter (CDM) simulations readily produce haloes that follow the universal Navarro-Frenk-White (NFW) density profile with an inner slope, ρ ∝ r-α, with α = 1, recent simulations have found that when the free-streaming cut-off expected for the CDM model is resolved, the resulting haloes follow nearly power-law density profiles of α ∼ 1.5. In this paper, we study the formation of density cusps in haloes using idealized N-body simulations of the collapse of proto-haloes. When the proto-halo profile is initially cored due to particle free-streaming at high redshift, we universally find ∼r-1.5 profiles irrespective of the proto-halo profile slope outside the core and large-scale non-spherical perturbations. Quite in contrast, when the proto-halo has a power-law profile, then we obtain profiles compatible with the NFW shape when the density slope of the proto-halo patch is shallower than a critical value, αini ∼ 0.3, while the final slope can be steeper for αini ≳ 0.3. We further demonstrate that the r-1.5 profiles are sensitive to small-scale noise, which gradually drives them towards an inner slope of -1, where they become resilient to such perturbations. We demonstrate that the r-1.5 solutions are in hydrostatic equilibrium, largely consistent with a simple analytic model, and provide arguments that angular momentum appears to determine the inner slope.

A Universal Angular Momentum Profile for Dark Matter Halos

NASA Astrophysics Data System (ADS)

Liao, Shihong; Chen, Jianxiong; Chu, M.-C.

2017-07-01

The angular momentum distribution in dark matter halos and galaxies is a key ingredient in understanding their formation. Specifically, the internal distribution of angular momenta is closely related to the formation of disk galaxies. In this article, we use halos identified from a high-resolution simulation, the Bolshoi simulation, to study the spatial distribution of specific angular momenta, j(r,θ ). We show that by stacking halos with similar masses to increase the signal-to-noise ratio, the profile can be fitted as a simple function, j{(r,θ )={j}s{\\sin }2{(θ /{θ }s)(r/{r}s)}2/(1+r/{r}s)}4, with three free parameters, {j}s,{r}s, and {θ }s. Specifically, j s correlates with the halo mass M vir as {j}s\\propto {M}{vir}2/3, r s has a weak dependence on the halo mass as {r}s\\propto {M}{vir}0.040, and {θ }s is independent of M vir. This profile agrees with that from a rigid shell model, though its origin is unclear. Our universal specific angular momentum profile j(r,θ ) is useful in modeling the angular momenta of halos. Furthermore, by using an empirical stellar mass-halo mass relation, we can infer the average angular momentum distribution of a dark matter halo. The specific angular momentum-stellar mass relation within a halo computed from our profile is shown to share a similar shape as that from the observed disk galaxies.

Semi-empirical catalog of early-type galaxy-halo systems: dark matter density profiles, halo contraction and dark matter annihilation strength

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

Chae, Kyu-Hyun; Kravtsov, Andrey V.; Frieman, Joshua A.

With Sloan Digital Sky Survey galaxy data and halo data from up-to-date N-body simulations within the ΛCDM framework we construct a semi-empirical catalog (SEC) of early-type galaxy-halo systems by making a self-consistent bivariate statistical match of stellar mass (M{sub *}) and velocity dispersion (σ) with halo virial mass (M{sub vir}) as demonstrated here for the first time. We then assign stellar mass profile and velocity dispersion profile parameters to each system in the SEC using their observed correlations with M{sub *} and σ. Simultaneously, we solve for dark matter density profile of each halo using the spherical Jeans equation. Themore » resulting dark matter density profiles deviate in general from the dissipationless profile of Navarro-Frenk-White or Einasto and their mean inner density slope and concentration vary systematically with M{sub vir}. Statistical tests of the distribution of profiles at fixed M{sub vir} rule out the null hypothesis that it follows the distribution predicted by dissipationless N-body simulations for M{sub vir}∼<10{sup 13.5} {sup –} {sup 14.5} M{sub s}un. These dark matter profiles imply that dark matter density is, on average, enhanced significantly in the inner region of halos with M{sub vir}∼<10{sup 13.5} {sup –} {sup 14.5} M{sub s}un supporting halo contraction. The main characteristics of halo contraction are: (1) the mean dark matter density within the effective radius has increased by a factor varying systematically up to ≈ 3–4 at M{sub vir} = 10{sup 12} M{sub s}un, and (2) the inner density slope has a mean of (α) ≈ 1.3 with ρ{sub dm}(r)∝r{sup −α} and a halo-to-halo rms scatter of rms(α) ∼ 0.4–0.5 for 10{sup 12} M{sub s}un∼« less

Halo abundance matching: accuracy and conditions for numerical convergence

NASA Astrophysics Data System (ADS)

Klypin, Anatoly; Prada, Francisco; Yepes, Gustavo; Heß, Steffen; Gottlöber, Stefan

2015-03-01

Accurate predictions of the abundance and clustering of dark matter haloes play a key role in testing the standard cosmological model. Here, we investigate the accuracy of one of the leading methods of connecting the simulated dark matter haloes with observed galaxies- the halo abundance matching (HAM) technique. We show how to choose the optimal values of the mass and force resolution in large volume N-body simulations so that they provide accurate estimates for correlation functions and circular velocities for haloes and their subhaloes - crucial ingredients of the HAM method. At the 10 per cent accuracy, results converge for ˜50 particles for haloes and ˜150 particles for progenitors of subhaloes. In order to achieve this level of accuracy a number of conditions should be satisfied. The force resolution for the smallest resolved (sub)haloes should be in the range (0.1-0.3)rs, where rs is the scale radius of (sub)haloes. The number of particles for progenitors of subhaloes should be ˜150. We also demonstrate that the two-body scattering plays a minor role for the accuracy of N-body simulations thanks to the relatively small number of crossing-times of dark matter in haloes, and the limited force resolution of cosmological simulations.

Length dependence of a halo orthosis on cervical immobilization.

PubMed

Triggs, K J; Ballock, R T; Byrne, T; Garfin, S R

1993-02-01

This study was designed to observe the length dependence of a well-molded fiberglass body cast attached to a halo on motion restriction in an unstable cadaveric cervical spine. Also, by using this technique, comparison between the immobilization provided by a body cast and that provided by a standard premolded polyethylene halo vest could be made. Extreme cervical instability was created on adult cadavers. A halo ring was applied and then attached to a fiberglass body cast or to a polyethylene halo vest. Sequential lateral cervical radiographs were obtained during maximum flexion as the body cast was shortened from the level of the iliac crests to the level of the xiphoid process. Radiographic motion was also assessed within the polyethylene halo vest. Results revealed minimal motion difference as the fiberglass body cast was sequentially shortened. In contrast, motions within the polyethylene halo vest were variable. These results suggest that cervical immobilization may be relatively independent of support structure length and that immobilization can be maintained by a well-fitting halo vest extending to the level of the xiphoid process.

Optimal linear reconstruction of dark matter from halo catalogues

DOE PAGES

Cai, Yan -Chuan; Bernstein, Gary; Sheth, Ravi K.

2011-04-01

The dark matter lumps (or "halos") that contain galaxies have locations in the Universe that are to some extent random with respect to the overall matter distributions. We investigate how best to estimate the total matter distribution from the locations of the halos. We derive the weight function w(M) to apply to dark-matter haloes that minimizes the stochasticity between the weighted halo distribution and its underlying mass density field. The optimal w(M) depends on the range of masses of halos being used. While the standard biased-Poisson model of the halo distribution predicts that bias weighting is optimal, the simple factmore » that the mass is comprised of haloes implies that the optimal w(M) will be a mixture of mass-weighting and bias-weighting. In N-body simulations, the Poisson estimator is up to 15× noisier than the optimal. Optimal weighting could make cosmological tests based on the matter power spectrum or cross-correlations much more powerful and/or cost effective.« less

Convergence properties of halo merger trees; halo and substructure merger rates across cosmic history

NASA Astrophysics Data System (ADS)

Poole, Gregory B.; Mutch, Simon J.; Croton, Darren J.; Wyithe, Stuart

2017-12-01

We introduce GBPTREES: an algorithm for constructing merger trees from cosmological simulations, designed to identify and correct for pathological cases introduced by errors or ambiguities in the halo finding process. GBPTREES is built upon a halo matching method utilizing pseudo-radial moments constructed from radially sorted particle ID lists (no other information is required) and a scheme for classifying merger tree pathologies from networks of matches made to-and-from haloes across snapshots ranging forward-and-backward in time. Focusing on SUBFIND catalogues for this work, a sweep of parameters influencing our merger tree construction yields the optimal snapshot cadence and scanning range required for converged results. Pathologies proliferate when snapshots are spaced by ≲0.128 dynamical times; conveniently similar to that needed for convergence of semi-analytical modelling, as established by Benson et al. Total merger counts are converged at the level of ∼5 per cent for friends-of-friends (FoF) haloes of size np ≳ 75 across a factor of 512 in mass resolution, but substructure rates converge more slowly with mass resolution, reaching convergence of ∼10 per cent for np ≳ 100 and particle mass mp ≲ 109 M⊙. We present analytic fits to FoF and substructure merger rates across nearly all observed galactic history (z ≤ 8.5). While we find good agreement with the results presented by Fakhouri et al. for FoF haloes, a slightly flatter dependence on merger ratio and increased major merger rates are found, reducing previously reported discrepancies with extended Press-Schechter estimates. When appropriately defined, substructure merger rates show a similar mass ratio dependence as FoF rates, but with stronger mass and redshift dependencies for their normalization.

Two-halo term in stacked thermal Sunyaev-Zel'dovich measurements: Implications for self-similarity

NASA Astrophysics Data System (ADS)

Hill, J. Colin; Baxter, Eric J.; Lidz, Adam; Greco, Johnny P.; Jain, Bhuvnesh

2018-04-01

The relation between the mass and integrated electron pressure of galaxy group and cluster halos can be probed by stacking maps of the thermal Sunyaev-Zel'dovich (tSZ) effect. Perhaps surprisingly, recent observational results have indicated that the scaling relation between integrated pressure and mass follows the prediction of simple, self-similar models down to halo masses as low as 1 012.5 M⊙ . Hydrodynamical simulations that incorporate energetic feedback processes suggest that gas should be depleted from such low-mass halos, thus decreasing their tSZ signal relative to self-similar predictions. Here, we build on the modeling of V. Vikram, A. Lidz, and B. Jain, Mon. Not. R. Astron. Soc. 467, 2315 (2017), 10.1093/mnras/stw3311 to evaluate the bias in the interpretation of stacked tSZ measurements due to the signal from correlated halos (the "two-halo" term), which has generally been neglected in the literature. We fit theoretical models to a measurement of the tSZ-galaxy group cross-correlation function, accounting explicitly for the one- and two-halo contributions. We find moderate evidence of a deviation from self-similarity in the pressure-mass relation, even after marginalizing over conservative miscentering effects. We explore pressure-mass models with a break at 1 014 M⊙, as well as other variants. We discuss and test for sources of uncertainty in our analysis, in particular a possible bias in the halo mass estimates and the coarse resolution of the Planck beam. We compare our findings with earlier analyses by exploring the extent to which halo isolation criteria can reduce the two-halo contribution. Finally, we show that ongoing third-generation cosmic microwave background experiments will explicitly resolve the one-halo term in low-mass groups; our methodology can be applied to these upcoming data sets to obtain a clear answer to the question of self-similarity and an improved understanding of hot gas in low-mass halos.

Comparative genomics and evolution of eukaryotic phospholipidbiosynthesis

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

Lykidis, Athanasios

2006-12-01

Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymesmore » and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.« less

Hierarchical Galaxy Growth and Scatter in the Stellar Mass-Halo Mass Relation

NASA Astrophysics Data System (ADS)

Gu, Meng; Conroy, Charlie; Behroozi, Peter

2016-12-01

The relation between galaxies and dark matter halos reflects the combined effects of many distinct physical processes. Observations indicate that the z = 0 stellar mass-halo mass (SMHM) relation has remarkably small scatter in stellar mass at fixed halo mass (≲0.2 dex), with little dependence on halo mass. We investigate the origins of this scatter by combining N-body simulations with observational constraints on the SMHM relation. We find that at the group and cluster scale ({M}{vir}\\gt {10}14 {M}⊙ ) the scatter due purely to hierarchical assembly is ≈ 0.16 dex, which is comparable to recent direct observational estimates. At lower masses, mass buildup since z≈ 2 is driven largely by in situ growth. We include a model for the in situ buildup of stellar mass and find that an intrinsic scatter in this growth channel of 0.2 dex produces a relation between scatter and halo mass that is consistent with observations from {10}12 {M}⊙ \\lt {M}{vir}\\lt {10}14.75 {M}⊙ . The approximately constant scatter across a wide range of halo masses at z = 0 thus appears to be a coincidence, as it is determined largely by in situ growth at low masses and by hierarchical assembly at high masses. These results indicate that the scatter in the SMHM relation can provide unique insight into the regularity of the galaxy formation process.

Null Environmental Effects of the Cosmic Web on Dark Matter Halo Properties

NASA Astrophysics Data System (ADS)

Goh, Tze; Primack, Joel; Aragon-Calvo, Miguel; Hellinger, Doug; Rodriguez-Puebla, Aldo; Lee, Christoph; Eckleholm, Elliot; Johnston, Kathryn

2018-01-01

We study the effects of the cosmic web environment (filaments, voids and walls) and environmental density on key properties of dark matter halos at redshift z = 0 using the Bolshoi-Planck ΛCDM. The z=0 Bolshoi-Planck simulation is analysed into filaments, voids and walls using the SpineWeb method, as well as VIDE method, both of which use Voronoi tessellation and the watershed transform. The key halo properties that we study are the mass accretion rate, spin parameter, concentration, prolateness, scale factor of the last major merger, and scale factor when the halo had half of its z=0 mass. For all these properties, we find that there is no discernible difference between the halo properties in filaments, walls or voids when compared at the same environmental density. As a result, we conclude that environmental density is the core attribute that affects these properties. This conclusion is in line with recent findings that properties of galaxies in redshift surveys are independent of their cosmic web environment at the same environmental density. We also find that the local web environment of the Milky Way and the Andromeda galaxy near the centre of a cosmic wall does not appear to have any effect on the key properties of these galaxies' dark matter halos, although we find that it is rather rare to have such massive halos near the centre of a relatively small cosmic wall.

Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics

PubMed Central

Louis, Alexandra; Nguyen, Nga Thi Thuy; Muffato, Matthieu; Roest Crollius, Hugues

2015-01-01

The Genomicus web server (http://www.genomicus.biologie.ens.fr/genomicus) is a visualization tool allowing comparative genomics in four different phyla (Vertebrate, Fungi, Metazoan and Plants). It provides access to genomic information from extant species, as well as ancestral gene content and gene order for vertebrates and flowering plants. Here we present the new features available for vertebrate genome with a focus on new graphical tools. The interface to enter the database has been improved, two pairwise genome comparison tools are now available (KaryoView and MatrixView) and the multiple genome comparison tools (PhyloView and AlignView) propose three new kinds of representation and a more intuitive menu. These new developments have been implemented for Genomicus portal dedicated to vertebrates. This allows the analysis of 68 extant animal genomes, as well as 58 ancestral reconstructed genomes. The Genomicus server also provides access to ancestral gene orders, to facilitate evolutionary and comparative genomics studies, as well as computationally predicted regulatory interactions, thanks to the representation of conserved non-coding elements with their putative gene targets. PMID:25378326

Isobar analog states (IAS), double isobar analog states (DIAS), configuration states (CS), and double configuration states (DCS) in halo nuclei. Halo isomers

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

Izosimov, I. N., E-mail: izosimov@jinr.ru

2015-10-15

It has been shown that IAS, DIAS, CS, and DCS can simultaneously have n-n, n-p, and p-p halo components in their wave functions. Differences in halo structure of the excited and ground states can result in the formation of isomers (halo-isomers). Both the Borromean and tango halo types can be observed for n-p configurations of atomic nuclei. The structure of the ground and excited states with different isospin quantum number in halo like nuclei is discussed. B(Mλ) and B(Eλ) for γ-transitions in {sup 6,7,8}Li, {sup 8,9,10}Be, {sup 8,10,11}B, {sup 10,11,12,13,14}C, {sup 13,14,15,16,17}N, {sup 15,16,17,19}O, and {sup 17}F are analyzed. Specialmore » attention is given to nuclei whose ground state does not exhibit halo structure but the excited state may have one.« less

A universal genomic coordinate translator for comparative genomics

PubMed Central

2014-01-01

Background Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Results Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of

A universal genomic coordinate translator for comparative genomics.

PubMed

Zamani, Neda; Sundström, Görel; Meadows, Jennifer R S; Höppner, Marc P; Dainat, Jacques; Lantz, Henrik; Haas, Brian J; Grabherr, Manfred G

2014-06-30

Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across

THE HALO OCCUPATION DISTRIBUTION OF SDSS QUASARS

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

Richardson, Jonathan; Chatterjee, Suchetana; Nagai, Daisuke

2012-08-10

We present an estimate of the projected two-point correlation function (2PCF) of quasars in the Sloan Digital Sky Survey (SDSS) over the full range of one- and two-halo scales, 0.02 h{sup -1} Mpc < r{sub p} < 120 h{sup -1} Mpc. This was achieved by combining data from SDSS DR7 on large scales and Hennawi et al. (with appropriate statistical corrections) on small scales. Our combined clustering sample is the largest spectroscopic quasar clustering sample to date, containing {approx}48, 000 quasars in the redshift range 0.4 {approx}< z {approx}< 2.5 with median redshift 1.4. We interpret these precise 2PCF measurementsmore » within the halo occupation distribution (HOD) framework and constrain the occupation functions of central and satellite quasars in dark matter halos. In order to explain the small-scale clustering, the HOD modeling requires that a small fraction of z {approx} 1.4 quasars, f{sub sat} = (7.4 {+-} 1.4) Multiplication-Sign 10{sup -4}, be satellites in dark matter halos. At z {approx} 1.4, the median masses of the host halos of central and satellite quasars are constrained to be M{sub cen} = 4.1{sup +0.3}{sub -0.4} Multiplication-Sign 10{sup 12} h{sup -1} M{sub Sun} and M{sub sat} = 3.6{sup +0.8}{sub -1.0} Multiplication-Sign 10{sup 14} h{sup -1} M{sub Sun }, respectively. To investigate the redshift evolution of the quasar-halo relationship, we also perform HOD modeling of the projected 2PCF measured by Shen et al. for SDSS quasars with median redshift 3.2. We find tentative evidence for an increase in the mass scale of quasar host halos-the inferred median mass of halos hosting central quasars at z {approx} 3.2 is M{sub cen} = 14.1{sup +5.8}{sub -6.9} Multiplication-Sign 10{sup 12} h{sup -1} M{sub Sun }. The cutoff profiles of the mean occupation functions of central quasars reveal that quasar luminosity is more tightly correlated with halo mass at higher redshifts. The average quasar duty cycle around the median host halo mass is inferred to be f

Initial sequencing and comparative analysis of the mouse genome

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

Waterston, Robert H.; Lindblad-Toh, Kerstin; Birney, Ewan

2002-12-15

The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of themore » genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.« less

PLAZA 3.0: an access point for plant comparative genomics.

PubMed

Proost, Sebastian; Van Bel, Michiel; Vaneechoutte, Dries; Van de Peer, Yves; Inzé, Dirk; Mueller-Roeber, Bernd; Vandepoele, Klaas

2015-01-01

Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Evolutionary and comparative analyses of the soybean genome

PubMed Central

Cannon, Steven B.; Shoemaker, Randy C.

2012-01-01

The soybean genome assembly has been available since the end of 2008. Significant features of the genome include large, gene-poor, repeat-dense pericentromeric regions, spanning roughly 57% of the genome sequence; a relatively large genome size of ~1.15 billion bases; remnants of a genome duplication that occurred ~13 million years ago (Mya); and fainter remnants of older polyploidies that occurred ~58 Mya and >130 Mya. The genome sequence has been used to identify the genetic basis for numerous traits, including disease resistance, nutritional characteristics, and developmental features. The genome sequence has provided a scaffold for placement of many genomic feature elements, both from within soybean and from related species. These may be accessed at several websites, including http://www.phytozome.net, http://soybase.org, http://comparative-legumes.org, and http://www.legumebase.brc.miyazaki-u.ac.jp. The taxonomic position of soybean in the Phaseoleae tribe of the legumes means that there are approximately two dozen other beans and relatives that have undergone independent domestication, and which may have traits that will be useful for transfer to soybean. Methods of translating information between species in the Phaseoleae range from design of markers for marker assisted selection, to transformation with Agrobacterium or with other experimental transformation methods. PMID:23136483

Clouds Dominate the Galactic Halo

NASA Astrophysics Data System (ADS)

2003-01-01

Using the exquisite sensitivity of the National Science Foundation's Robert C. Byrd Green Bank Telescope (GBT), astronomer Jay Lockman of the National Radio Astronomy Observatory (NRAO) in Green Bank, W. Va., has produced the best cross-section ever of the Milky Way Galaxy's diffuse halo of hydrogen gas. This image confirms the presence of discrete hydrogen clouds in the halo, and could help astronomers understand the origin and evolution of the rarefied atmosphere that surrounds our Galaxy. Lockman presented his findings at the American Astronomical Society meeting in Seattle, WA. Hydrogen Clouds Graphic Artist's Rendering of the Milky Way (background) with insert showing GBT image of cross-section of neutral atomic Hydrogen Credit: Kirk Woellert/National Science Foundation Patricia Smiley, NRAO. "The first observations with the Green Bank Telescope suggested that the hydrogen in the lower halo, the transition zone between the Milky Way and intergalactic space, is very clumpy," said Lockman. "The latest data confirm these results and show that instead of trailing away smoothly from the Galactic plane, a significant fraction of the hydrogen gas in the halo is concentrated in discrete clouds. There are even some filaments." Beyond the star-filled disk of the Milky Way, there exists an extensive yet diffuse halo of hydrogen gas. For years, astronomers have speculated about the origin and structure of this gas. "Even the existence of neutral hydrogen in the halo has been somewhat of a puzzle," Lockman remarked. "Unlike the Earth's atmosphere, which is hot enough to hold itself up against the force of gravity, the hydrogen in the halo is too cool to support itself against the gravitational pull of the Milky Way." Lockman points out that some additional factor has to be involved to get neutral hydrogen to such large distances from the Galactic plane. "This force could be cosmic rays, a supersonic wind, the blast waves from supernovae, or something we have not thought of

Precision measurement of the local bias of dark matter halos

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

Lazeyras, Titouan; Wagner, Christian; Schmidt, Fabian

2016-02-01

We present accurate measurements of the linear, quadratic, and cubic local bias of dark matter halos, using curved 'separate universe' N-body simulations which effectively incorporate an infinite-wavelength overdensity. This can be seen as an exact implementation of the peak-background split argument. We compare the results with the linear and quadratic bias measured from the halo-matter power spectrum and bispectrum, and find good agreement. On the other hand, the standard peak-background split applied to the Sheth and Tormen (1999) and Tinker et al. (2008) halo mass functions matches the measured linear bias parameter only at the level of 10%. The predictionmore » from the excursion set-peaks approach performs much better, which can be attributed to the stochastic moving barrier employed in the excursion set-peaks prediction. We also provide convenient fitting formulas for the nonlinear bias parameters b{sub 2}(b{sub 1}) and b{sub 3}(b{sub 1}), which work well over a range of redshifts.« less

The Mass and Absorption Columns of Galactic Gaseous Halos

NASA Astrophysics Data System (ADS)

Qu, Zhijie; Bregman, Joel N.

2018-03-01

The galactic gaseous halo is a gas reservoir for the interstellar medium in the galaxy disk, supplying materials for star formation. We developed a gaseous halo model connecting the galaxy disk and the gaseous halo by assuming that the star formation rate on the disk is balanced by the radiative cooling rate of the gaseous halo, including stellar feedback. In addition to a single-temperature gaseous halo in collisional ionization equilibrium, we also consider the photoionization effect and a steady-state cooling model. Photoionization is important for modifying the ion distribution in low-mass galaxies and in the outskirts of massive galaxies due to the low densities. The multiphase cooling model dominates the region within the cooling radius, where t cooling = t Hubble. Our model reproduces most of the observed high ionization state ions for a wide range of galaxy masses (i.e., O VI, O VII, Ne VIII, Mg X, and O VIII). We find that the O VI column density has a narrow range around ≈1014 cm‑2 for halo masses from M ⋆ ≈ 3 × 1010 M ⊙ to 6 × 1012 M ⊙, which is consistent with some but not all observational studies. For galaxies with halo masses ≲3 × 1011 M ⊙, photoionization produces most of the O VI, while for more massive galaxies, the O VI is from the medium that is cooling from higher temperatures. Fitting the Galactic (Milky-Way) O VII and O VIII suggests a gaseous halo model where the metallicity is ≈0.55 Z ⊙ and the gaseous halo has a maximum temperature of ≈1.9 × 106 K. This gaseous halo model does not close the census of baryonic material within R 200.

Constraining the noise-free distribution of halo spin parameters

NASA Astrophysics Data System (ADS)

Benson, Andrew J.

2017-11-01

Any measurement made using an N-body simulation is subject to noise due to the finite number of particles used to sample the dark matter distribution function, and the lack of structure below the simulation resolution. This noise can be particularly significant when attempting to measure intrinsically small quantities, such as halo spin. In this work, we develop a model to describe the effects of particle noise on halo spin parameters. This model is calibrated using N-body simulations in which the particle noise can be treated as a Poisson process on the underlying dark matter distribution function, and we demonstrate that this calibrated model reproduces measurements of halo spin parameter error distributions previously measured in N-body convergence studies. Utilizing this model, along with previous measurements of the distribution of halo spin parameters in N-body simulations, we place constraints on the noise-free distribution of halo spins. We find that the noise-free median spin is 3 per cent lower than that measured directly from the N-body simulation, corresponding to a shift of approximately 40 times the statistical uncertainty in this measurement arising purely from halo counting statistics. We also show that measurement of the spin of an individual halo to 10 per cent precision requires at least 4 × 104 particles in the halo - for haloes containing 200 particles, the fractional error on spins measured for individual haloes is of order unity. N-body simulations should be viewed as the results of a statistical experiment applied to a model of dark matter structure formation. When viewed in this way, it is clear that determination of any quantity from such a simulation should be made through forward modelling of the effects of particle noise.

Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more

PubMed Central

Fumoto, Masaki; Miyazaki, Satoru; Sugawara, Hideaki

2002-01-01

Genome Information Broker (GIB) is a powerful tool for the study of comparative genomics. GIB allows users to retrieve and display partial and/or whole genome sequences together with the relevant biological annotation. GIB has accumulated all the completed microbial genome and has recently been expanded to include Arabidopsis thaliana genome data from DDBJ/EMBL/GenBank. In the near future, hundreds of genome sequences will be determined. In order to handle such huge data, we have enhanced the GIB architecture by using XML, CORBA and distributed RDBs. We introduce the new GIB here. GIB is freely accessible at http://gib.genes.nig.ac.jp/. PMID:11752256

The f ( R ) halo mass function in the cosmic web

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

Braun-Bates, F. von; Winther, H.A.; Alonso, D.

An important indicator of modified gravity is the effect of the local environment on halo properties. This paper examines the influence of the local tidal structure on the halo mass function, the halo orientation, spin and the concentration-mass relation. We use the excursion set formalism to produce a halo mass function conditional on large-scale structure. Our simple model agrees well with simulations on large scales at which the density field is linear or weakly non-linear. Beyond this, our principal result is that f ( R ) does affect halo abundances, the halo spin parameter and the concentration-mass relationship in anmore » environment-independent way, whereas we find no appreciable deviation from \\text(ΛCDM) for the mass function with fixed environment density, nor the alignment of the orientation and spin vectors of the halo to the eigenvectors of the local cosmic web. There is a general trend for greater deviation from \\text(ΛCDM) in underdense environments and for high-mass haloes, as expected from chameleon screening.« less

Observation and analysis of halo current in EAST

NASA Astrophysics Data System (ADS)

Chen, Da-Long; Shen, Biao; Qian, Jin-Ping; Sun, You-Wen; Liu, Guang-Jun; Shi, Tong-Hui; Zhuang, Hui-Dong; Xiao, Bing-Jia

2014-06-01

Plasma in a typically elongated cross-section tokamak (for example, EAST) is inherently unstable against vertical displacement. When plasma loses the vertical position control, it moves downward or upward, leading to disruption, and a large halo current is generated helically in EAST typically in the scrape-off layer. When flowing into the vacuum vessel through in-vessel components, the halo current will give rise to a large J × B force acting on the vessel and the in-vessel components. In EAST VDE experiment, part of the eddy current is measured in halo sensors, due to the large loop voltage. Primary experimental data demonstrate that the halo current first lands on the outer plate and then flows clockwise, and the analysis of the information indicates that the maximum halo current estimated in EAST is about 0.4 times the plasma current and the maximum value of TPF × Ih/IP0 is 0.65, furthermore Ih/Ip0 and TPF × Ih/Ip0 tend to increase with the increase of Ip0. The test of the strong gas injection system shows good success in increasing the radiated power, which may be effective in reducing the halo current.

Statistics of Dark Matter Halos from Gravitational Lensing.

PubMed

Jain; Van Waerbeke L

2000-02-10

We present a new approach to measure the mass function of dark matter halos and to discriminate models with differing values of Omega through weak gravitational lensing. We measure the distribution of peaks from simulated lensing surveys and show that the lensing signal due to dark matter halos can be detected for a wide range of peak heights. Even when the signal-to-noise ratio is well below the limit for detection of individual halos, projected halo statistics can be constrained for halo masses spanning galactic to cluster halos. The use of peak statistics relies on an analytical model of the noise due to the intrinsic ellipticities of source galaxies. The noise model has been shown to accurately describe simulated data for a variety of input ellipticity distributions. We show that the measured peak distribution has distinct signatures of gravitational lensing, and its non-Gaussian shape can be used to distinguish models with different values of Omega. The use of peak statistics is complementary to the measurement of field statistics, such as the ellipticity correlation function, and is possibly not susceptible to the same systematic errors.

Unmixing the Galactic halo with RR Lyrae tagging

NASA Astrophysics Data System (ADS)

Belokurov, V.; Deason, A. J.; Koposov, S. E.; Catelan, M.; Erkal, D.; Drake, A. J.; Evans, N. W.

2018-06-01

We show that tagging RR Lyrae stars according to their location in the period-amplitude diagram can be used to shed light on the genesis of the Galactic stellar halo. The mixture of RR Lyrae of ab type, separated into classes along the lines suggested by Oosterhoff, displays a strong and coherent evolution with Galactocentric radius. The change in the RR Lyrae composition appears to coincide with the break in the halo's radial density profile at ˜25 kpc. Using simple models of the stellar halo, we establish that at least three different types of accretion events are necessary to explain the observed RRab behaviour. Given that there exists a correlation between the RRab class fraction and the total stellar content of a dwarf satellite, we hypothesize that the field halo RRab composition is controlled by the mass of the progenitor contributing the bulk of the stellar debris at the given radius. This idea is tested against a suite of cosmological zoom-in simulations of Milky Way-like stellar halo formation. Finally, we study some of the most prominent stellar streams in the Milky Way halo and demonstrate that their RRab class fractions follow the trends established previously.

Remapping dark matter halo catalogues between cosmological simulations

NASA Astrophysics Data System (ADS)

Mead, A. J.; Peacock, J. A.

2014-05-01

We present and test a method for modifying the catalogue of dark matter haloes produced from a given cosmological simulation, so that it resembles the result of a simulation with an entirely different set of parameters. This extends the method of Angulo & White, which rescales the full particle distribution from a simulation. Working directly with the halo catalogue offers an advantage in speed, and also allows modifications of the internal structure of the haloes to account for non-linear differences between cosmologies. Our method can be used directly on a halo catalogue in a self-contained manner without any additional information about the overall density field; although the large-scale displacement field is required by the method, this can be inferred from the halo catalogue alone. We show proof of concept of our method by rescaling a matter-only simulation with no baryon acoustic oscillation (BAO) features to a more standard Λ cold dark matter model containing a cosmological constant and a BAO signal. In conjunction with the halo occupation approach, this method provides a basis for the rapid generation of mock galaxy samples spanning a wide range of cosmological parameters.

A Guide to the PLAZA 3.0 Plant Comparative Genomic Database.

PubMed

Vandepoele, Klaas

2017-01-01

PLAZA 3.0 is an online resource for comparative genomics and offers a versatile platform to study gene functions and gene families or to analyze genome organization and evolution in the green plant lineage. Starting from genome sequence information for over 35 plant species, precomputed comparative genomic data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, and genomic colinearity information within and between species. Complementary functional data sets, a Workbench, and interactive visualization tools are available through a user-friendly web interface, making PLAZA an excellent starting point to translate sequence or omics data sets into biological knowledge. PLAZA is available at http://bioinformatics.psb.ugent.be/plaza/ .

THE EFFECTS OF ANGULAR MOMENTUM ON HALO PROFILES

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

Lentz, Erik W; Rosenberg, Leslie J; Quinn, Thomas R, E-mail: lentze@phys.washington.edu, E-mail: ljrosenberg@phys.washington.edu, E-mail: trq@astro.washington.edu

2016-05-10

The near universality of DM halo density profiles provided by N -body simulations proved to be robust against changes in total mass density, power spectrum, and some forms of initial velocity dispersion. Here we study the effects of coherently spinning up an isolated DM-only progenitor on halo structure. Halos with spins within several standard deviations of the simulated mean ( λ ≲ 0.20) produce profiles with negligible deviations from the universal form. Only when the spin becomes quite large ( λ ≳ 0.20) do departures become evident. The angular momentum distribution also exhibits a near universal form, which is alsomore » independent of halo spin up to λ ≲ 0.20. A correlation between these epidemic profiles and the presence of a strong bar in the virialized halo is also observed. These bar structures bear resemblance to the radial orbit instability in the rotationless limit.« less

Development of an Automatic Detection Program of Halo CMEs

NASA Astrophysics Data System (ADS)

Choi, K.; Park, M. Y.; Kim, J.

2017-12-01

The front-side halo CMEs are the major cause for large geomagnetic storms. Halo CMEs can result in damage to satellites, communication, electrical transmission lines and power systems. Thus automated techniques for detecting and analysing Halo CMEs from coronagraph data are of ever increasing importance for space weather monitoring and forecasting. In this study, we developed the algorithm that can automatically detect and do image processing the Halo CMEs in the images from the LASCO C3 coronagraph on board the SOHO spacecraft. With the detection algorithm, we derived the geometric and kinematical parameters of halo CMEs, such as source location, width, actual CME speed and arrival time at 21.5 solar radii.

Comparative genomics of parasitic silkworm microsporidia reveal an association between genome expansion and host adaptation

PubMed Central

2013-01-01

Background Microsporidian Nosema bombycis has received much attention because the pébrine disease of domesticated silkworms results in great economic losses in the silkworm industry. So far, no effective treatment could be found for pébrine. Compared to other known Nosema parasites, N. bombycis can unusually parasitize a broad range of hosts. To gain some insights into the underlying genetic mechanism of pathological ability and host range expansion in this parasite, a comparative genomic approach is conducted. The genome of two Nosema parasites, N. bombycis and N. antheraeae (an obligatory parasite to undomesticated silkworms Antheraea pernyi), were sequenced and compared with their distantly related species, N. ceranae (an obligatory parasite to honey bees). Results Our comparative genomics analysis show that the N. bombycis genome has greatly expanded due to the following three molecular mechanisms: 1) the proliferation of host-derived transposable elements, 2) the acquisition of many horizontally transferred genes from bacteria, and 3) the production of abundnant gene duplications. To our knowledge, duplicated genes derived not only from small-scale events (e.g., tandem duplications) but also from large-scale events (e.g., segmental duplications) have never been seen so abundant in any reported microsporidia genomes. Our relative dating analysis further indicated that these duplication events have arisen recently over very short evolutionary time. Furthermore, several duplicated genes involving in the cytotoxic metabolic pathway were found to undergo positive selection, suggestive of the role of duplicated genes on the adaptive evolution of pathogenic ability. Conclusions Genome expansion is rarely considered as the evolutionary outcome acting on those highly reduced and compact parasitic microsporidian genomes. This study, for the first time, demonstrates that the parasitic genomes can expand, instead of shrink, through several common molecular mechanisms

Historic halo displays as weather indicator: Criteria and examples

NASA Astrophysics Data System (ADS)

Neuhäuser, Dagmar L.; Neuhäuser, Ralph

2016-04-01

There are numerous celestial signs reported in historic records, many of them refer to atmospheric ("sub-lunar") phenomena, such as ice halos and aurorae. In an interdisciplinary collaboration between astrophysics and cultural astronomy, we noticed that celestial observations including meteorological phenomena are often misinterpreted, mostly due to missing genuine criteria: especially ice crystal halos were recorded frequently in past centuries for religious reasons, but are mistaken nowadays often for other phenomena like aurorae. Ice halo displays yield clear information on humidity and temperature in certain atmospheric layers, and thereby indicate certain weather patterns. Ancient so-called rain makers used halo observations for weather forecast; e.g., a connection between certain halo displays and rain a few day later is statistically significant. Ice halos exist around sun and moon and are reported for both (they can stay for several days): many near, middle, and far eastern records from day- and night-time include such observations with high frequency. (Partly based on publications on halos by D.L. Neuhäuser & R. Neuhäuser, available at http://www.astro.uni-jena.de/index.php/terra-astronomy.html)

Populating dark matter haloes with galaxies: comparing the 2dFGRS with mock galaxy redshift surveys

NASA Astrophysics Data System (ADS)

Yang, Xiaohu; Mo, H. J.; Jing, Y. P.; van den Bosch, Frank C.; Chu, YaoQuan

2004-06-01

In two recent papers, we developed a powerful technique to link the distribution of galaxies to that of dark matter haloes by considering halo occupation numbers as a function of galaxy luminosity and type. In this paper we use these distribution functions to populate dark matter haloes in high-resolution N-body simulations of the standard ΛCDM cosmology with Ωm= 0.3, ΩΛ= 0.7 and σ8= 0.9. Stacking simulation boxes of 100 h-1 Mpc and 300 h-1 Mpc with 5123 particles each we construct mock galaxy redshift surveys out to a redshift of z= 0.2 with a numerical resolution that guarantees completeness down to 0.01L*. We use these mock surveys to investigate various clustering statistics. The predicted two-dimensional correlation function ξ(rp, π) reveals clear signatures of redshift space distortions. The projected correlation functions for galaxies with different luminosities and types, derived from ξ(rp, π), match the observations well on scales larger than ~3 h-1 Mpc. On smaller scales, however, the model overpredicts the clustering power by about a factor two. Modelling the `finger-of-God' effect on small scales reveals that the standard ΛCDM model predicts pairwise velocity dispersions (PVD) that are ~400 km s-1 too high at projected pair separations of ~1 h-1 Mpc. A strong velocity bias in massive haloes, with bvel≡σgal/σdm~ 0.6 (where σgal and σdm are the velocity dispersions of galaxies and dark matter particles, respectively) can reduce the predicted PVD to the observed level, but does not help to resolve the overprediction of clustering power on small scales. Consistent results can be obtained within the standard ΛCDM model only when the average mass-to-light ratio of clusters is of the order of 1000 (M/L)solar in the B-band. Alternatively, as we show by a simple approximation, a ΛCDM model with σ8~= 0.75 may also reproduce the observational results. We discuss our results in light of the recent WMAP results and the constraints on σ8 obtained

Globular Cluster Contributions to the Galactic Halo

NASA Astrophysics Data System (ADS)

Martell, Sarah; Grebel, Eva; Lai, David

2010-08-01

The goal of this project is to confirm chemically that globular clusters are the source of as much as half the population of the Galactic halo. Using moderate-resolution spectroscopy from the SEGUE survey, we have identified a previously unknown population of halo field giants with distinctly strong CN features. CN variations are typically only observed in globular clusters, so these stars are interpreted as immigrants to the halo that originally formed in globular clusters. In one night of Keck/HIRES time, we will obtain high-quality, high- resolution spectra for five such stars, and determine abundances of O, Na, Mg, Al, alpha, iron-peak and neutron-capture elements. With this information we can state clearly whether these unusual CN-strong halo stars carry the full abundance pattern seen in CN-strong globular cluster stars, with depleted C, O, and Mg and enhanced N, Na, and Al. This type of coarse ``chemical tagging'' will allow a clearer division of the Galactic halo into contributions from globular clusters and from dwarf galaxies, and will place constraints on theoretical models of globular cluster formation and evolution.

Sensitivity of the halo nuclei-12C elastic scattering at incident nucleon energy 800 MeV to the halo density distribution

NASA Astrophysics Data System (ADS)

Hassan, M. A. M.; Nour El-Din, M. S. M.; Ellithi, A.; Hosny, H.; Salama, T. N. E.

2017-10-01

In the framework of Glauber optical limit approximation where Coulomb effect is taken into account, the elastic scattering differential cross section for halo nuclei with {}^{12}{C} at 800 MeV/N has been calculated. Its sensitivity to the halo densities and the root mean square of the core and halo is the main goal of the current study. The projectile nuclei are taken to be one-neutron and two-neutron halo. The calculations are carried out for Gaussian-Gaussian, Gaussian-Oscillator and Gaussian-2 s phenomenological densities for each considered projectile in the mass number range 6-29. Also included a comparison between the obtained results of phenomenological densities and the results within the microscopic densities LSSM of {}6{He} and {}^{11}{Li} and microscopic densities GCM of {}^{11}{Be} where the density of the target nucleus {}^{12}{C} obtained from electron-{}^{12}{C} scattering is used. The zero range approximation is considered in the calculations. We found that the sensitivity of elastic scattering differential cross section to the halo density is clear if the nucleus appears as two clear different clusters, core and halo.

COGNAT: a web server for comparative analysis of genomic neighborhoods.

PubMed

Klimchuk, Olesya I; Konovalov, Kirill A; Perekhvatov, Vadim V; Skulachev, Konstantin V; Dibrova, Daria V; Mulkidjanian, Armen Y

2017-11-22

In prokaryotic genomes, functionally coupled genes can be organized in conserved gene clusters enabling their coordinated regulation. Such clusters could contain one or several operons, which are groups of co-transcribed genes. Those genes that evolved from a common ancestral gene by speciation (i.e. orthologs) are expected to have similar genomic neighborhoods in different organisms, whereas those copies of the gene that are responsible for dissimilar functions (i.e. paralogs) could be found in dissimilar genomic contexts. Comparative analysis of genomic neighborhoods facilitates the prediction of co-regulated genes and helps to discern different functions in large protein families. We intended, building on the attribution of gene sequences to the clusters of orthologous groups of proteins (COGs), to provide a method for visualization and comparative analysis of genomic neighborhoods of evolutionary related genes, as well as a respective web server. Here we introduce the COmparative Gene Neighborhoods Analysis Tool (COGNAT), a web server for comparative analysis of genomic neighborhoods. The tool is based on the COG database, as well as the Pfam protein families database. As an example, we show the utility of COGNAT in identifying a new type of membrane protein complex that is formed by paralog(s) of one of the membrane subunits of the NADH:quinone oxidoreductase of type 1 (COG1009) and a cytoplasmic protein of unknown function (COG3002). This article was reviewed by Drs. Igor Zhulin, Uri Gophna and Igor Rogozin.

The slight spin of the old stellar halo

NASA Astrophysics Data System (ADS)

Deason, Alis J.; Belokurov, Vasily; Koposov, Sergey E.; Gómez, Facundo A.; Grand, Robert J.; Marinacci, Federico; Pakmor, Rüdiger

2017-09-01

We combine Gaia data release 1 astrometry with Sloan Digital Sky Survey (SDSS) images taken some ˜10-15 years earlier, to measure proper motions of stars in the halo of our Galaxy. The SDSS-Gaia proper motions have typical statistical errors of 2 mas yr-1 down to r ˜ 20 mag, and are robust to variations with magnitude and colour. Armed with this exquisite set of halo proper motions, we identify RR Lyrae, blue horizontal branch (BHB), and K giant stars in the halo, and measure their net rotation with respect to the Galactic disc. We find evidence for a gently rotating prograde signal (〈Vϕ〉 ˜ 5-25 km s-1) in the halo stars, which shows little variation with Galactocentric radius out to 50 kpc. The average rotation signal for the three populations is 〈Vϕ〉 = 14 ± 2 ± 10 (syst.) km s-1. There is also tentative evidence for a kinematic correlation with metallicity, whereby the metal richer BHB and K giant stars have slightly stronger prograde rotation than the metal poorer stars. Using the Auriga simulation suite, we find that the old (T >10 Gyr) stars in the simulated haloes exhibit mild prograde rotation, with little dependence on radius or metallicity, in general agreement with the observations. The weak halo rotation suggests that the Milky Way has a minor in situ halo component, and has undergone a relatively quiet accretion history.

The Prevalence of the 22 deg Halo in Cirrus Clouds

NASA Technical Reports Server (NTRS)

Diedenhoven, vanBastiaan

2014-01-01

Halos at 22 deg from the sun attributed to randomly-orientated, pristine hexagonal crystals are frequently observed through ice clouds. These frequent sightings of halos formed by pristine crystals pose an apparent inconsistency with the dominance of distorted, nonpristine ice crystals indicated by in situ and remote sensing data. Furthermore, the 46 deg halo, which is associated with pristine hexagonal crystals as well, is observed far less frequently than the 22 deg halo. Considering that plausible mechanisms that could cause crystal distortion such as aggregation, sublimation, riming and collisions are stochastic processes that likely lead to distributions of crystals with varying distortion levels, here the presence of the 22 deg and 46 deg halo features in phase functions of mixtures of pristine and distorted hexagonal ice crystals is examined. We conclude that the 22 deg halo feature is generally present if the contribution by pristine crystals to the total scattering cross section is greater than only about 10% in the case of compact particles or columns, and greater than about 40% for plates. The 46 deg halo feature is present only if the mean distortion level is low and the contribution of pristine crystals to the total scattering cross section is above about 20%, 50% and 70%, in the case of compact crystals, plates and columns, respectively. These results indicate that frequent sightings of 22 deg halos are not inconsistent with the observed dominance of distorted, non-pristine ice crystals. Furthermore, the low mean distortion levels and large contributions by pristine crystals needed to produce the 461 halo features provide a potential explanation of the common sighting of the 22 deg halo without any detectable 46 deg halo.

Nucleoid halo expansion indirectly measures DNA damage in single cells.

PubMed

Thomas, E A; Thomas, C A

1989-07-01

A simple test has been developed that measures how much DNA damage has occurred in a single mammalian cell. The procedure is based on the microscopic examination of "halos" of nucleoids that adhere to coverslips. Nucleoids are produced by flowing salt solutions containing detergents over the attached cells. The nucleoid halos are thought to be a tangle of loops of free DNA that emanate from the remnants of the nucleus. When visualized by staining with ethidium bromide the nucleoid halos first expand, and then contract as the concentration of ethidium increases. Exposure of nucleoids to very low levels of DNA chain-breaking treatments results in the incremental expansion of the halos to a maximum of 15 microns or more. Our assay is based upon quantitating the degree of halo expansion. If intact cells are exposed to DNA-damaging treatments, then allowed increasing periods of post-treatment growth before forming nucleoids, the DNA repair processes result first in expanded and then in contracted halos. By admixing a supercoiled plasma DNA of known length (38 kb) to nucleoids with contracted halos, the fractional halo expansion and the fraction of surviving plasmid supercoils can be measured from the same solution. Use of photodynamic DNA damage showed that the halo expansion was 11.6 times more sensitive than plasmid relaxation. Use of gamma-irradiation showed that the halo expansion was 3.6 times more sensitive than plasmid relaxation. The latter value demonstrates that one break per 137,000 bp results in the expansion of the halos to 63% of their maximal value. We estimate that this method will detect about 5000 breaks per nucleus containing 5 x 10(9) bp.

Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics.

PubMed

Louis, Alexandra; Nguyen, Nga Thi Thuy; Muffato, Matthieu; Roest Crollius, Hugues

2015-01-01

The Genomicus web server (http://www.genomicus.biologie.ens.fr/genomicus) is a visualization tool allowing comparative genomics in four different phyla (Vertebrate, Fungi, Metazoan and Plants). It provides access to genomic information from extant species, as well as ancestral gene content and gene order for vertebrates and flowering plants. Here we present the new features available for vertebrate genome with a focus on new graphical tools. The interface to enter the database has been improved, two pairwise genome comparison tools are now available (KaryoView and MatrixView) and the multiple genome comparison tools (PhyloView and AlignView) propose three new kinds of representation and a more intuitive menu. These new developments have been implemented for Genomicus portal dedicated to vertebrates. This allows the analysis of 68 extant animal genomes, as well as 58 ancestral reconstructed genomes. The Genomicus server also provides access to ancestral gene orders, to facilitate evolutionary and comparative genomics studies, as well as computationally predicted regulatory interactions, thanks to the representation of conserved non-coding elements with their putative gene targets. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

DO NOT FORGET THE FOREST FOR THE TREES: THE STELLAR-MASS HALO-MASS RELATION IN DIFFERENT ENVIRONMENTS

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

Tonnesen, Stephanie; Cen, Renyue, E-mail: stonnes@gmail.com, E-mail: cen@astro.princeton.edu

2015-10-20

The connection between dark matter halos and galactic baryons is often not well constrained nor well resolved in cosmological hydrodynamical simulations. Thus, halo occupation distribution models that assign galaxies to halos based on halo mass are frequently used to interpret clustering observations, even though it is well known that the assembly history of dark matter halos is related to their clustering. In this paper we use high-resolution hydrodynamical cosmological simulations to compare the halo and stellar mass growth of galaxies in a large-scale overdensity to those in a large-scale underdensity (on scales of about 20 Mpc). The simulation reproduces assemblymore » bias, in which halos have earlier formation times in overdense environments than in underdense regions. We find that the ratio of stellar mass to halo mass is larger in overdense regions in central galaxies residing in halos with masses between 10{sup 11} and 10{sup 12.9} M{sub ⊙}. When we force the local density (within 2 Mpc) at z = 0 to be the same for galaxies in the large-scale over- and underdensities, we find the same results. We posit that this difference can be explained by a combination of earlier formation times, more interactions at early times with neighbors, and more filaments feeding galaxies in overdense regions. This result puts the standard practice of assigning stellar mass to halos based only on their mass, rather than considering their larger environment, into question.« less

Identification and Molecular Characterization of Genes Coding Pharmaceutically Important Enzymes from Halo-Thermo Tolerant Bacillus

PubMed Central

Safary, Azam; Moniri, Rezvan; Hamzeh-Mivehroud, Maryam; Dastmalchi, Siavoush

2016-01-01

Purpose: Robust pharmaceutical and industrial enzymes from extremophile microorganisms are main source of enzymes with tremendous stability under harsh conditions which make them potential tools for commercial and biotechnological applications. Methods: The genome of a Gram-positive halo-thermotolerant Bacillus sp. SL1, new isolate from Saline Lake, was investigated for the presence of genes coding for potentially pharmaceutical enzymes. We determined gene sequences for the enzymes laccase (CotA), l-asparaginase (ansA3, ansA1), glutamate-specific endopeptidase (blaSE), l-arabinose isomerase (araA2), endo-1,4-β mannosidase (gmuG), glutaminase (glsA), pectate lyase (pelA), cellulase (bglC1), aldehyde dehydrogenase (ycbD) and allantoinases (pucH) in the genome of Bacillus sp. SL1. Results: Based on the DNA sequence alignment results, six of the studied enzymes of Bacillus sp. SL-1 showed 100% similarity at the nucleotide level to the same genes of B. licheniformis 14580 demonstrating extensive organizational relationship between these two strains. Despite high similarities between the B. licheniformis and Bacillus sp. SL-1 genomes, there are minor differences in the sequences of some enzyme. Approximately 30% of the enzyme sequences revealed more than 99% identity with some variations in nucleotides leading to amino acid substitution in protein sequences. Conclusion: Molecular characterization of this new isolate provides useful information regarding evolutionary relationship between B. subtilis and B. licheniformis species. Since, the most industrial processes are often performed in harsh conditions, enzymes from such halo-thermotolerant bacteria may provide economically and industrially appealing biocatalysts to be used under specific physicochemical situations in medical, pharmaceutical, chemical and other industries. PMID:28101462

Identification and Molecular Characterization of Genes Coding Pharmaceutically Important Enzymes from Halo-Thermo Tolerant Bacillus.

PubMed

Safary, Azam; Moniri, Rezvan; Hamzeh-Mivehroud, Maryam; Dastmalchi, Siavoush

2016-12-01

Purpose: Robust pharmaceutical and industrial enzymes from extremophile microorganisms are main source of enzymes with tremendous stability under harsh conditions which make them potential tools for commercial and biotechnological applications. Methods: The genome of a Gram-positive halo-thermotolerant Bacillus sp. SL1, new isolate from Saline Lake, was investigated for the presence of genes coding for potentially pharmaceutical enzymes. We determined gene sequences for the enzymes laccase (CotA), l-asparaginase (ansA3, ansA1), glutamate-specific endopeptidase (blaSE), l-arabinose isomerase (araA2), endo-1,4-β mannosidase (gmuG), glutaminase (glsA), pectate lyase (pelA), cellulase (bglC1), aldehyde dehydrogenase (ycbD) and allantoinases (pucH) in the genome of Bacillus sp. SL1. Results: Based on the DNA sequence alignment results, six of the studied enzymes of Bacillus sp. SL-1 showed 100% similarity at the nucleotide level to the same genes of B. licheniformis 14580 demonstrating extensive organizational relationship between these two strains. Despite high similarities between the B. licheniformis and Bacillus sp. SL-1 genomes, there are minor differences in the sequences of some enzyme. Approximately 30% of the enzyme sequences revealed more than 99% identity with some variations in nucleotides leading to amino acid substitution in protein sequences. Conclusion: Molecular characterization of this new isolate provides useful information regarding evolutionary relationship between B. subtilis and B. licheniformis species. Since, the most industrial processes are often performed in harsh conditions, enzymes from such halo-thermotolerant bacteria may provide economically and industrially appealing biocatalysts to be used under specific physicochemical situations in medical, pharmaceutical, chemical and other industries.

Uncovering the hidden iceberg structure of the Galactic halo

NASA Astrophysics Data System (ADS)

Moss, Vanessa A.; Di Teodoro, Enrico M.; McClure-Griffiths, Naomi M.; Lockman, Felix; Pisano, D. J.; Price, Daniel; Rees, Glen

2018-01-01

How the Milky Way gets its gas and keeps its measured star formation rate going are both long-standing mysteries in Galactic studies, with important implications for galaxy evolution across the Universe. I will present our recent discovery of two populations of neutral hydrogen (HI) in the halo of the Milky Way: 1) a narrow line-width dense population typical of the majority of bright high velocity cloud (HVC) components, and 2) a fainter, broad line-width diffuse population that aligns well with the population found in very sensitive pointings such as in Lockman et al. (2002). From our existing data, we concluded that the diffuse population likely outweighs the dense HI by a factor of 3. This discovery of diffuse HI, which appears to be prevalent throughout the halo, takes us closer to solving the Galactic mystery of accretion and reveals a gaseous neutral halo hidden from the view of most large-scale surveys. We are currently carrying out deep Parkes observations to investigate these results further, in order to truly uncover the nature of the diffuse HI and determine whether our 3:1 ratio (based on the limited existing data) is consistent with what is seen when Parkes and the 140 ft Green Bank telescope are employed at comparable sensitivity. With these data, through a combination of both known and new sightline measurements, we aim to reveal the structure of the Galactic halo in more detail than ever before.

Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

PubMed Central

2011-01-01

Background Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. Results We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. Conclusions A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae. PMID:21226921

Abort Options for Human Missions to Earth-Moon Halo Orbits

NASA Technical Reports Server (NTRS)

Jesick, Mark C.

2013-01-01

Abort trajectories are optimized for human halo orbit missions about the translunar libration point (L2), with an emphasis on the use of free return trajectories. Optimal transfers from outbound free returns to L2 halo orbits are numerically optimized in the four-body ephemeris model. Circumlunar free returns are used for direct transfers, and cislunar free returns are used in combination with lunar gravity assists to reduce propulsive requirements. Trends in orbit insertion cost and flight time are documented across the southern L2 halo family as a function of halo orbit position and free return flight time. It is determined that the maximum amplitude southern halo incurs the lowest orbit insertion cost for direct transfers but the maximum cost for lunar gravity assist transfers. The minimum amplitude halo is the most expensive destination for direct transfers but the least expensive for lunar gravity assist transfers. The on-orbit abort costs for three halos are computed as a function of abort time and return time. Finally, an architecture analysis is performed to determine launch and on-orbit vehicle requirements for halo orbit missions.

Comparative and demographic analysis of orangutan genomes

PubMed Central

Locke, Devin P.; Hillier, LaDeana W.; Warren, Wesley C.; Worley, Kim C.; Nazareth, Lynne V.; Muzny, Donna M.; Yang, Shiaw-Pyng; Wang, Zhengyuan; Chinwalla, Asif T.; Minx, Pat; Mitreva, Makedonka; Cook, Lisa; Delehaunty, Kim D.; Fronick, Catrina; Schmidt, Heather; Fulton, Lucinda A.; Fulton, Robert S.; Nelson, Joanne O.; Magrini, Vincent; Pohl, Craig; Graves, Tina A.; Markovic, Chris; Cree, Andy; Dinh, Huyen H.; Hume, Jennifer; Kovar, Christie L.; Fowler, Gerald R.; Lunter, Gerton; Meader, Stephen; Heger, Andreas; Ponting, Chris P.; Marques-Bonet, Tomas; Alkan, Can; Chen, Lin; Cheng, Ze; Kidd, Jeffrey M.; Eichler, Evan E.; White, Simon; Searle, Stephen; Vilella, Albert J.; Chen, Yuan; Flicek, Paul; Ma, Jian; Raney, Brian; Suh, Bernard; Burhans, Richard; Herrero, Javier; Haussler, David; Faria, Rui; Fernando, Olga; Darré, Fleur; Farré, Domènec; Gazave, Elodie; Oliva, Meritxell; Navarro, Arcadi; Roberto, Roberta; Capozzi, Oronzo; Archidiacono, Nicoletta; Valle, Giuliano Della; Purgato, Stefania; Rocchi, Mariano; Konkel, Miriam K.; Walker, Jerilyn A.; Ullmer, Brygg; Batzer, Mark A.; Smit, Arian F. A.; Hubley, Robert; Casola, Claudio; Schrider, Daniel R.; Hahn, Matthew W.; Quesada, Victor; Puente, Xose S.; Ordoñez, Gonzalo R.; López-Otín, Carlos; Vinar, Tomas; Brejova, Brona; Ratan, Aakrosh; Harris, Robert S.; Miller, Webb; Kosiol, Carolin; Lawson, Heather A.; Taliwal, Vikas; Martins, André L.; Siepel, Adam; RoyChoudhury, Arindam; Ma, Xin; Degenhardt, Jeremiah; Bustamante, Carlos D.; Gutenkunst, Ryan N.; Mailund, Thomas; Dutheil, Julien Y.; Hobolth, Asger; Schierup, Mikkel H.; Chemnick, Leona; Ryder, Oliver A.; Yoshinaga, Yuko; de Jong, Pieter J.; Weinstock, George M.; Rogers, Jeffrey; Mardis, Elaine R.; Gibbs, Richard A.; Wilson, Richard K.

2011-01-01

“Orangutan” is derived from the Malay term “man of the forest” and aptly describes the Southeast Asian great apes native to Sumatra and Borneo. The orangutan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orangutan draft genome assembly and short read sequence data from five Sumatran and five Bornean orangutan genomes. Our analyses reveal that, compared to other primates, the orangutan genome has many unique features. Structural evolution of the orangutan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe the first primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orangutan genome structure. Orangutans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400k years ago (ya), is more recent than most previous studies and underscores the complexity of the orangutan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities

Dark energy and extended dark matter halos

NASA Astrophysics Data System (ADS)

Chernin, A. D.; Teerikorpi, P.; Valtonen, M. J.; Dolgachev, V. P.; Domozhilova, L. M.; Byrd, G. G.

2012-03-01

The cosmological mean matter (dark and baryonic) density measured in the units of the critical density is Ωm = 0.27. Independently, the local mean density is estimated to be Ωloc = 0.08-0.23 from recent data on galaxy groups at redshifts up to z = 0.01-0.03 (as published by Crook et al. 2007, ApJ, 655, 790 and Makarov & Karachentsev 2011, MNRAS, 412, 2498). If the lower values of Ωloc are reliable, as Makarov & Karachentsev and some other observers prefer, does this mean that the Local Universe of 100-300 Mpc across is an underdensity in the cosmic matter distribution? Or could it nevertheless be representative of the mean cosmic density or even be an overdensity due to the Local Supercluster therein. We focus on dark matter halos of groups of galaxies and check how much dark mass the invisible outer layers of the halos are able to host. The outer layers are usually devoid of bright galaxies and cannot be seen at large distances. The key factor which bounds the size of an isolated halo is the local antigravity produced by the omnipresent background of dark energy. A gravitationally bound halo does not extend beyond the zero-gravity surface where the gravity of matter and the antigravity of dark energy balance, thus defining a natural upper size of a system. We use our theory of local dynamical effects of dark energy to estimate the maximal sizes and masses of the extended dark halos. Using data from three recent catalogs of galaxy groups, we show that the calculated mass bounds conform with the assumption that a significant amount of dark matter is located in the invisible outer parts of the extended halos, sufficient to fill the gap between the observed and expected local matter density. Nearby groups of galaxies and the Virgo cluster have dark halos which seem to extend up to their zero-gravity surfaces. If the extended halo is a common feature of gravitationally bound systems on scales of galaxy groups and clusters, the Local Universe could be typical or even

Galactic googly: the rotation-metallicity bias in the inner stellar halo of the Milky Way

NASA Astrophysics Data System (ADS)

Kafle, Prajwal R.; Sharma, Sanjib; Robotham, Aaron S. G.; Pradhan, Raj K.; Guglielmo, Magda; Davies, Luke J. M.; Driver, Simon P.

2017-09-01

The first and second moments of stellar velocities encode important information about the formation history of the Galactic halo. However, due to the lack of tangential motion and inaccurate distances of the halo stars, the velocity moments in the Galactic halo have largely remained 'known unknowns'. Fortunately, our off-centric position within the Galaxy allows us to estimate these moments in the galactocentric frame using the observed radial velocities of the stars alone. We use these velocities coupled with the hierarchical Bayesian scheme, which allows easy marginalization over the missing data (the proper motion, and uncertainty-free distance and line-of-sight velocity), to measure the velocity dispersions, orbital anisotropy (β) and streaming motion (vrot) of the halo main-sequence turn-off (MSTO) and K-giant (KG) stars in the inner stellar halo (r ≲ 15 kpc). We study the metallicity bias in kinematics of the halo stars and observe that the comparatively metal-rich ([Fe/H] > -1.4) and the metal-poor ([Fe/H] ≤ -1.4) MSTO samples show a clear systematic difference in vrot ˜ 20-40 km s - 1, depending on how restrictive the spatial cuts to cull the disc contamination are. The bias is also detected in KG samples but with less certainty. Both MSTO and KG populations suggest that the inner stellar halo of the Galaxy is radially biased I.e. σr > σθ or σϕ and β ≃ 0.5. The apparent metallicity contrariety in the rotation velocity among the halo sub-populations supports the co-existence of multiple populations in the galactic halo that may have formed through distinct formation scenarios, I.e. in situ versus accretion.

Whole genome annotation and comparative genomic analyses of bio-control fungus Purpureocillium lilacinum.

PubMed

Prasad, Pushplata; Varshney, Deepti; Adholeya, Alok

2015-11-25

The fungus Purpureocillium lilacinum is widely known as a biological control agent against plant parasitic nematodes. This research article consists of genomic annotation of the first draft of whole genome sequence of P. lilacinum. The study aims to decipher the putative genetic components of the fungus involved in nematode pathogenesis by performing comparative genomic analysis with nine closely related fungal species in Hypocreales. de novo genomic assembly was done and a total of 301 scaffolds were constructed for P. lilacinum genomic DNA. By employing structural genome prediction models, 13, 266 genes coding for proteins were predicted in the genome. Approximately 73% of the predicted genes were functionally annotated using Blastp, InterProScan and Gene Ontology. A 14.7% fraction of the predicted genes shared significant homology with genes in the Pathogen Host Interactions (PHI) database. The phylogenomic analysis carried out using maximum likelihood RAxML algorithm provided insight into the evolutionary relationship of P. lilacinum. In congruence with other closely related species in the Hypocreales namely, Metarhizium spp., Pochonia chlamydosporia, Cordyceps militaris, Trichoderma reesei and Fusarium spp., P. lilacinum has large gene sets coding for G-protein coupled receptors (GPCRs), proteases, glycoside hydrolases and carbohydrate esterases that are required for degradation of nematode-egg shell components. Screening of the genome by Antibiotics & Secondary Metabolite Analysis Shell (AntiSMASH) pipeline indicated that the genome potentially codes for a variety of secondary metabolites, possibly required for adaptation to heterogeneous lifestyles reported for P. lilacinum. Significant up-regulation of subtilisin-like serine protease genes in presence of nematode eggs in quantitative real-time analyses suggested potential role of serine proteases in nematode pathogenesis. The data offer a better understanding of Purpureocillium lilacinum genome and will

Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes.

PubMed

Staton, Margaret; Zhebentyayeva, Tetyana; Olukolu, Bode; Fang, Guang Chen; Nelson, Dana; Carlson, John E; Abbott, Albert G

2015-10-05

Chinese chestnut (Castanea mollissima) has emerged as a model species for the Fagaceae family with extensive genomic resources including a physical map, a dense genetic map and quantitative trait loci (QTLs) for chestnut blight resistance. These resources enable comparative genomics analyses relative to model plants. We assessed the degree of conservation between the chestnut genome and other well annotated and assembled plant genomic sequences, focusing on the QTL regions of most interest to the chestnut breeding community. The integrated physical and genetic map of Chinese chestnut has been improved to now include 858 shared sequence-based markers. The utility of the integrated map has also been improved through the addition of 42,970 BAC (bacterial artificial chromosome) end sequences spanning over 26 million bases of the estimated 800 Mb chestnut genome. Synteny between chestnut and ten model plant species was conducted on a macro-syntenic scale using sequences from both individual probes and BAC end sequences across the chestnut physical map. Blocks of synteny with chestnut were found in all ten reference species, with the percent of the chestnut physical map that could be aligned ranging from 10 to 39 %. The integrated genetic and physical map was utilized to identify BACs that spanned the three previously identified QTL regions conferring blight resistance. The clones were pooled and sequenced, yielding 396 sequence scaffolds covering 13.9 Mbp. Comparative genomic analysis on a microsytenic scale, using the QTL-associated genomic sequence, identified synteny from chestnut to other plant genomes ranging from 5.4 to 12.9 % of the genome sequences aligning. On both the macro- and micro-synteny levels, the peach, grape and poplar genomes were found to be the most structurally conserved with chestnut. Interestingly, these results did not strictly follow the expectation that decreased phylogenetic distance would correspond to increased levels of genome

Comparative whole genome analysis of six diagnostic brucellaphages.

PubMed

Farlow, Jason; Filippov, Andrey A; Sergueev, Kirill V; Hang, Jun; Kotorashvili, Adam; Nikolich, Mikeljon P

2014-05-15

Whole genome sequencing of six diagnostic brucellaphages, Tbilisi (Tb), Firenze (Fz), Weybridge (Wb), S708, Berkeley (Bk) and R/C, was followed with genomic comparisons including recently described genomes of the Tb phage from Mexico (TbM) and Pr phage to elucidate genomic diversity and candidate host range determinants. Comparative whole genome analysis revealed high sequence homogeneity among these brucellaphage genomes and resolved three genetic groups consistent with defined host range phenotypes. Group I was composed of Tb and Fz phages that are predominantly lytic for Brucella abortus and Brucella neotomae; Group II included Bk, R/C, and Pr phages that are lytic mainly for B. abortus, Brucella melitensis and Brucella suis; Group III was composed of Wb and S708 phages that are lytic for B. suis, B. abortus and B. neotomae. We found that the putative phage collar protein is a variable locus with features that may be contributing to the host specificities exhibited by different brucellaphage groups. The presence of several candidate host range determinants is illustrated herein for future dissection of the differential host specificity observed among these phages. Published by Elsevier B.V.

Angular momentum properties of haloes and their baryon content in the Illustris simulation

NASA Astrophysics Data System (ADS)

Zjupa, Jolanta; Springel, Volker

2017-04-01

The angular momentum properties of virialized dark matter haloes have been measured with good statistics in collisionless N-body simulations, but an equally accurate analysis of the baryonic spin is still missing. We employ the Illustris simulation suite, one of the first simulations of galaxy formation with full hydrodynamics that produces a realistic galaxy population in a sizeable volume, to quantify the baryonic spin properties for more than ˜320 000 haloes. We first compare the systematic differences between different spin parameter and halo definitions, and the impact of sample selection criteria on the derived properties. We confirm that dark-matter-only haloes exhibit a close to self-similar spin distribution in mass and redshift of lognormal form. However, the physics of galaxy formation radically changes the baryonic spin distribution. While the dark matter component remains largely unaffected, strong trends with mass and redshift appear for the spin of diffuse gas and the formed stellar component. With time, the baryons staying bound to the halo develop a misalignment of their spin vector with respect to dark matter, and increase their specific angular momentum by a factor of ˜1.3 in the non-radiative case and ˜1.8 in the full physics setup at z = 0. We show that this enhancement in baryonic spin can be explained by the combined effect of specific angular momentum transfer from dark matter on to gas during mergers and from feedback expelling low specific angular momentum gas from the halo. Our results challenge certain models for spin evolution and underline the significant changes induced by baryonic physics in the structure of haloes.

What is the Milky Way outer halo made of?

NASA Astrophysics Data System (ADS)

Jablonka, Pascale; Battaglia, G.

2018-06-01

In a framework where galaxies form hierarchically, extended stellar haloes are predicted to be an ubiquitous feature around Milky Way-like galaxies and to consist mainly of the shredded stellar component of smaller galactic systems. The type of accreted stellar systems are expected to vary according to the specific accretion and merging history of a given galaxy, and so is the fraction of stars formed in-situ versus accreted. Analysis of the chemical properties of Milky Way halo stars out to large Galactocentric radii can provide important insights into the properties of the environment in which the stars that contributed to the build-up of different regions of the Milky Way stellar halo formed. In this talk I will focus on the outer regions of the Milky Way stellar halo, and present results from a program aimed at determining chemical abundances of halo stars with large present-day Galactocentric distances, $>$15 kpc. The data-set consists of high resolution spectra for 28 red giant branch stars covering a wide metallicity range.We show that the ratio of $\\alpha$-elements over Fe as a function of [Fe/H] for our sample of outer halo stars is not dissimilar from the pattern shown by MW halo stars from solar neighborhood samples. On the other hand, significant differences appear at [Fe/H]$\\gtrsim -1.5$ when considering chemical abundance ratios such as [Ba/Fe], [Na/Fe], [Ni/Fe], [Eu/Fe], [Ba/Y]. Qualitatively, this type of chemical abundance trends are observed in massive dwarf galaxies, such as Sagittarius and the Large Magellanic Cloud. This appears to suggest a larger contribution in the outer halo of stars formed in an environment with high initial star formation rate and already polluted by asymptotic giant branch stars with respect to inner halo samples.

Revealing modified gravity signals in matter and halo hierarchical clustering

NASA Astrophysics Data System (ADS)

Hellwing, Wojciech A.; Koyama, Kazuya; Bose, Benjamin; Zhao, Gong-Bo

2017-07-01

We use a set of N-body simulations employing a modified gravity (MG) model with Vainshtein screening to study matter and halo hierarchical clustering. As test-case scenarios we consider two normal branch Dvali-Gabadadze-Porrati (nDGP) gravity models with mild and strong growth rate enhancement. We study higher-order correlation functions ξn(R ) up to n =9 and associated reduced cumulants Sn(R )≡ξn(R )/σ (R )2n -2. We find that the matter probability distribution functions are strongly affected by the fifth force on scales up to 50 h-1 Mpc , and the deviations from general relativity (GR) are maximized at z =0 . For reduced cumulants Sn, we find that at small scales R ≤6 h-1 Mpc the MG is characterized by lower values, with the deviation growing from 7% in the reduced skewness up to even 40% in S5. To study the halo clustering we use a simple abundance matching and divide haloes into thee fixed number density samples. The halo two-point functions are weakly affected, with a relative boost of the order of a few percent appearing only at the smallest pair separations (r ≤5 h-1 Mpc ). In contrast, we find a strong MG signal in Sn(R )'s, which are enhanced compared to GR. The strong model exhibits a >3 σ level signal at various scales for all halo samples and in all cumulants. In this context, we find that the reduced kurtosis to be an especially promising cosmological probe of MG. Even the mild nDGP model leaves a 3 σ imprint at small scales R ≤3 h-1 Mpc , while the stronger model deviates from a GR signature at nearly all scales with a significance of >5 σ . Since the signal is persistent in all halo samples and over a range of scales, we advocate that the reduced kurtosis estimated from galaxy catalogs can potentially constitute a strong MG-model discriminatory as well as GR self-consistency test.

Benchmark of 3D halo neutral simulation in TRANSP and FIDASIM and application to projected neutral-beam-heated NSTX-U plasmas

NASA Astrophysics Data System (ADS)

Liu, D.; Medley, S. S.; Gorelenkova, M. V.; Heidbrink, W. W.; Stagner, L.

2014-10-01

A cloud of halo neutrals is created in the vicinity of beam footprint during the neutral beam injection and the halo neutral density can be comparable with beam neutral density. Proper modeling of halo neutrals is critical to correctly interpret neutral particle analyzers (NPA) and fast ion D-alpha (FIDA) signals since these signals strongly depend on local beam and halo neutral density. A 3D halo neutral model has been recently developed and implemented inside TRANSP code. The 3D halo neutral code uses a ``beam-in-a-box'' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce thermal halo neutrals that are tracked through successive halo neutral generations until an ionization event occurs or a descendant halo exits the box. A benchmark between 3D halo neural model in TRANSP and in FIDA/NPA synthetic diagnostic code FIDASIM is carried out. Detailed comparison of halo neutral density profiles from two codes will be shown. The NPA and FIDA simulations with and without 3D halos are applied to projections of plasma performance for the National Spherical Tours eXperiment-Upgrade (NSTX-U) and the effects of halo neutral density on NPA and FIDA signal amplitude and profile will be presented. Work supported by US DOE.

Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia

PubMed Central

Capilla, Laia; Sánchez-Guillén, Rosa Ana; Farré, Marta; Paytuví-Gallart, Andreu; Malinverni, Roberto; Ventura, Jacint; Larkin, Denis M.

2016-01-01

Abstract Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints. PMID:28175287

Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia.

PubMed

Capilla, Laia; Sánchez-Guillén, Rosa Ana; Farré, Marta; Paytuví-Gallart, Andreu; Malinverni, Roberto; Ventura, Jacint; Larkin, Denis M; Ruiz-Herrera, Aurora

2016-12-01

Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.

Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates

PubMed Central

Yuan, Bo; Liu, Pengfei; Gupta, Aditya; Beck, Christine R.; Tejomurtula, Anusha; Campbell, Ian M.; Gambin, Tomasz; Simmons, Alexandra D.; Withers, Marjorie A.; Harris, R. Alan; Rogers, Jeffrey; Schwartz, David C.; Lupski, James R.

2015-01-01

Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM# 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85% of the NPHP1 cases—about 80% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual’s susceptibility to acquiring disease-associated alleles. PMID:26641089

Studying Dust Scattering Halos with Galactic X-ray Binaries

NASA Astrophysics Data System (ADS)

Beeler, Doreen; Corrales, Lia; Heinz, Sebastian

2018-01-01

Dust is an important part of the interstellar medium (ISM) and contributes to the formation of stars and planets. Since the advent of modern X-ray telescopes, Galactic X-ray point sources have permitted a closer look at all phases of the ISM. Interstellar metals from oxygen to iron — in both gas and dust form — are responsible for absorption and scattering of X-ray light. Dust scatters the light in a forward direction and creates a diffuse halo image surrounding many bright Galactic X-ray binaries. We use all the bright X-ray point sources available in the Chandra HETG archive to study dust scattering halos from the local ISM. We have described a data analysis pipeline using a combination of the data reduction software CIAO and Python. We compare our results from Chandra HETG and ACIS-I observations of a well studied dust scattering halo around GX 13+1, in order to characterize any systematic errors associated with the HETG data set. We describe how our data products will be used to measure ISM scaling relations for X-ray extinction, dust abundance, and dust-to-metal ratios.

Comparison of halo of 11Be, 15C, and 19C

NASA Astrophysics Data System (ADS)

Kharab, R.; Kumar, R.; Singh, P.; Sharma, H. C.

2007-12-01

We have compared the halo of 11Be, 15C, and 19C nuclei by analyzing the one-neutron stripping reaction data on the Be target at 60-, 54-, and 57-MeV/ A beam energies, respectively, within the framework of the eikonal approximation approach. The determination of effective range through the comparison of the total cross section data and prediction has revealed that the halo of 19C is the well developed, while that of 15C is the least and that of 11Be lies in between these two. The longitudinal momentum distribution data also strengthen these observations.

MIPSPlantsDB—plant database resource for integrative and comparative plant genome research

PubMed Central

Spannagl, Manuel; Noubibou, Octave; Haase, Dirk; Yang, Li; Gundlach, Heidrun; Hindemitt, Tobias; Klee, Kathrin; Haberer, Georg; Schoof, Heiko; Mayer, Klaus F. X.

2007-01-01

Genome-oriented plant research delivers rapidly increasing amount of plant genome data. Comprehensive and structured information resources are required to structure and communicate genome and associated analytical data for model organisms as well as for crops. The increase in available plant genomic data enables powerful comparative analysis and integrative approaches. PlantsDB aims to provide data and information resources for individual plant species and in addition to build a platform for integrative and comparative plant genome research. PlantsDB is constituted from genome databases for Arabidopsis, Medicago, Lotus, rice, maize and tomato. Complementary data resources for cis elements, repetive elements and extensive cross-species comparisons are implemented. The PlantsDB portal can be reached at . PMID:17202173

Velocity bias in the distribution of dark matter halos

NASA Astrophysics Data System (ADS)

Baldauf, Tobias; Desjacques, Vincent; Seljak, Uroš

2015-12-01

The standard formalism for the coevolution of halos and dark matter predicts that any initial halo velocity bias rapidly decays to zero. We argue that, when the purpose is to compute statistics like power spectra etc., the coupling in the momentum conservation equation for the biased tracers must be modified. Our new formulation predicts the constancy in time of any statistical halo velocity bias present in the initial conditions, in agreement with peak theory. We test this prediction by studying the evolution of a conserved halo population in N -body simulations. We establish that the initial simulated halo density and velocity statistics show distinct features of the peak model and, thus, deviate from the simple local Lagrangian bias. We demonstrate, for the first time, that the time evolution of their velocity is in tension with the rapid decay expected in the standard approach.

The age of the Milky Way inner halo.

PubMed

Kalirai, Jason S

2012-05-30

The Milky Way galaxy has several components, such as the bulge, disk and halo. Unravelling the assembly history of these stellar populations is often restricted because of difficulties in measuring accurate ages for low-mass, hydrogen-burning stars. Unlike these progenitors, white dwarf stars, the 'cinders' of stellar evolution, are remarkably simple objects and their fundamental properties can be measured with little ambiguity. Here I report observations of newly formed white dwarf stars in the halo of the Milky Way, and a separate analysis of archival data in the well studied 12.5-billion-year-old globular cluster Messier 4. I measure the mass distribution of the remnant stars and invert the stellar evolution process to develop a mathematical relation that links this final stellar mass to the mass of their immediate progenitors, and therefore to the age of the parent population. By applying this technique to a small sample of four nearby and kinematically confirmed halo white dwarf stars, I calculate the age of local field halo stars to be 11.4 ± 0.7 billion years. The oldest globular clusters formed 13.5 billion years ago. Future observations of newly formed white dwarf stars in the halo could be used to reduce the uncertainty, and to probe relative differences between the formation times of the youngest globular clusters and the inner halo.

ZOMG - III. The effect of halo assembly on the satellite population

NASA Astrophysics Data System (ADS)

Garaldi, Enrico; Romano-Díaz, Emilio; Borzyszkowski, Mikolaj; Porciani, Cristiano

2018-01-01

We use zoom hydrodynamical simulations to investigate the properties of satellites within galaxy-sized dark-matter haloes with different assembly histories. We consider two classes of haloes at redshift z = 0: 'stalled' haloes that assembled at z > 1 and 'accreting' ones that are still forming nowadays. Previously, we showed that the stalled haloes are embedded within thick filaments of the cosmic web, while the accreting ones lie where multiple thin filaments converge. We find that satellites in the two classes have both similar and different properties. Their mass spectra, radial count profiles, baryonic and stellar content, and the amount of material they shed are indistinguishable. However, the mass fraction locked in satellites is substantially larger for the accreting haloes as they experience more mergers at late times. The largest difference is found in the satellite kinematics. Substructures fall towards the accreting haloes along quasi-radial trajectories whereas an important tangential velocity component is developed, before accretion, while orbiting the filament that surrounds the stalled haloes. Thus, the velocity anisotropy parameter of the satellites (β) is positive for the accreting haloes and negative for the stalled ones. This signature enables us to tentatively categorize the Milky Way halo as stalled based on a recent measurement of β. Half of our haloes contain clusters of satellites with aligned orbital angular momenta corresponding to flattened structures in space. These features are not driven by baryonic physics and are only found in haloes hosting grand-design spiral galaxies, independently of their assembly history.

The globular cluster-dark matter halo connection

NASA Astrophysics Data System (ADS)

Boylan-Kolchin, Michael

2017-12-01

I present a simple phenomenological model for the observed linear scaling of the stellar mass in old globular clusters (GCs) with z = 0 halo mass in which the stellar mass in GCs scales linearly with progenitor halo mass at z = 6 above a minimum halo mass for GC formation. This model reproduces the observed MGCs-Mhalo relation at z = 0 and results in a prediction for the minimum halo mass at z = 6 required for hosting one GC: Mmin(z = 6) = 1.07 × 109 M⊙. Translated to z = 0, the mean threshold mass is Mhalo(z = 0) ≈ 2 × 1010 M⊙. I explore the observability of GCs in the reionization era and their contribution to cosmic reionization, both of which depend sensitively on the (unknown) ratio of GC birth mass to present-day stellar mass, ξ. Based on current detections of z ≳ 6 objects with M1500<-17, values of ξ > 10 are strongly disfavoured; this, in turn, has potentially important implications for GC formation scenarios. Even for low values of ξ, some observed high-z galaxies may actually be GCs, complicating estimates of reionization-era galaxy ultraviolet luminosity functions and constraints on dark matter models. GCs are likely important reionization sources if 5 ≲ ξ ≲ 10. I also explore predictions for the fraction of accreted versus in situ GCs in the local Universe and for descendants of systems at the halo mass threshold of GC formation (dwarf galaxies). An appealing feature of the model presented here is the ability to make predictions for GC properties based solely on dark matter halo merger trees.

Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology.

PubMed

Sharma, Archana; Satyanarayana, T

2013-01-01

With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review.

The Profile of the Galactic Halo from Pan-STARRS1 3π RR Lyrae

NASA Astrophysics Data System (ADS)

Hernitschek, Nina; Cohen, Judith G.; Rix, Hans-Walter; Sesar, Branimir; Martin, Nicolas F.; Magnier, Eugene; Wainscoat, Richard; Kaiser, Nick; Tonry, John L.; Kudritzki, Rolf-Peter; Hodapp, Klaus; Chambers, Ken; Flewelling, Heather; Burgett, William

2018-05-01

We characterize the spatial density of the Pan-STARRS1 (PS1) sample of Rrab stars to study the properties of the old Galactic stellar halo. This sample, containing 44,403 sources, spans galactocentric radii of 0.55 kpc ≤ R gc ≤ 141 kpc with a distance precision of 3% and thus is able to trace the halo out to larger distances than most previous studies. After excising stars that are attributed to dense regions such as stellar streams, the Galactic disk and bulge, and halo globular clusters, the sample contains ∼11,000 sources within 20 kpc ≤ R gc ≤ 131 kpc. We then apply forward modeling using Galactic halo profile models with a sample selection function. Specifically, we use ellipsoidal stellar density models ρ(l, b, R gc) with a constant and a radius-dependent halo flattening q(R gc). Assuming constant flattening q, the distribution of the sources is reasonably well fit by a single power law with n={4.40}-0.04+0.05 and q={0.918}-0.014+0.016 and comparably well fit by an Einasto profile with n={9.53}-0.28+0.27, an effective radius r eff = 1.07 ± 0.10 kpc, and a halo flattening of q = 0.923 ± 0.007. If we allow for a radius-dependent flattening q(R gc), we find evidence for a distinct flattening of q ∼ 0.8 of the inner halo at ∼25 kpc. Additionally, we find that the south Galactic hemisphere is more flattened than the north Galactic hemisphere. The results of our work are largely consistent with many earlier results (e.g., Watkins et al.; Iorio et al.). We find that the stellar halo, as traced in RR Lyrae stars, exhibits a substantial number of further significant over- and underdensities, even after masking all known overdensities.

Investigation of the halo-artifact in 68Ga-PSMA-11-PET/MRI.

PubMed

Heußer, Thorsten; Mann, Philipp; Rank, Christopher M; Schäfer, Martin; Dimitrakopoulou-Strauss, Antonia; Schlemmer, Heinz-Peter; Hadaschik, Boris A; Kopka, Klaus; Bachert, Peter; Kachelrieß, Marc; Freitag, Martin T

2017-01-01

Combined positron emission tomography (PET) and magnetic resonance imaging (MRI) targeting the prostate-specific membrane antigen (PSMA) with a 68Ga-labelled PSMA-analog (68Ga-PSMA-11) is discussed as a promising diagnostic method for patients with suspicion or history of prostate cancer. One potential drawback of this method are severe photopenic (halo-) artifacts surrounding the bladder and the kidneys in the scatter-corrected PET images, which have been reported to occur frequently in clinical practice. The goal of this work was to investigate the occurrence and impact of these artifacts and, secondly, to evaluate variants of the standard scatter correction method with regard to halo-artifact suppression. Experiments using a dedicated pelvis phantom were conducted to investigate whether the halo-artifact is modality-, tracer-, and/or concentration-dependent. Furthermore, 31 patients with history of prostate cancer were selected from an ongoing 68Ga-PSMA-11-PET/MRI study. For each patient, PET raw data were reconstructed employing six different variants of PET scatter correction: absolute scatter scaling, relative scatter scaling, and relative scatter scaling combined with prompt gamma correction, each of which was combined with a maximum scatter fraction (MaxSF) of MaxSF = 75% or MaxSF = 40%. Evaluation of the reconstructed images with regard to halo-artifact suppression was performed both quantitatively using statistical analysis and qualitatively by two independent readers. The phantom experiments did not reveal any modality-dependency (PET/MRI vs. PET/CT) or tracer-dependency (68Ga vs. 18F-FDG). Patient- and phantom-based data indicated that halo-artifacts derive from high organ-to-background activity ratios (OBR) between bladder/kidneys and surrounding soft tissue, with a positive correlation between OBR and halo size. Comparing different variants of scatter correction, reducing the maximum scatter fraction from the default value MaxSF = 75% to MaxSF = 40

Investigation of the halo-artifact in 68Ga-PSMA-11-PET/MRI

PubMed Central

Rank, Christopher M.; Schäfer, Martin; Dimitrakopoulou-Strauss, Antonia; Schlemmer, Heinz-Peter; Hadaschik, Boris A.; Kopka, Klaus; Bachert, Peter; Kachelrieß, Marc

2017-01-01

Objectives Combined positron emission tomography (PET) and magnetic resonance imaging (MRI) targeting the prostate-specific membrane antigen (PSMA) with a 68Ga-labelled PSMA-analog (68Ga-PSMA-11) is discussed as a promising diagnostic method for patients with suspicion or history of prostate cancer. One potential drawback of this method are severe photopenic (halo-) artifacts surrounding the bladder and the kidneys in the scatter-corrected PET images, which have been reported to occur frequently in clinical practice. The goal of this work was to investigate the occurrence and impact of these artifacts and, secondly, to evaluate variants of the standard scatter correction method with regard to halo-artifact suppression. Methods Experiments using a dedicated pelvis phantom were conducted to investigate whether the halo-artifact is modality-, tracer-, and/or concentration-dependent. Furthermore, 31 patients with history of prostate cancer were selected from an ongoing 68Ga-PSMA-11-PET/MRI study. For each patient, PET raw data were reconstructed employing six different variants of PET scatter correction: absolute scatter scaling, relative scatter scaling, and relative scatter scaling combined with prompt gamma correction, each of which was combined with a maximum scatter fraction (MaxSF) of MaxSF = 75% or MaxSF = 40%. Evaluation of the reconstructed images with regard to halo-artifact suppression was performed both quantitatively using statistical analysis and qualitatively by two independent readers. Results The phantom experiments did not reveal any modality-dependency (PET/MRI vs. PET/CT) or tracer-dependency (68Ga vs. 18F-FDG). Patient- and phantom-based data indicated that halo-artifacts derive from high organ-to-background activity ratios (OBR) between bladder/kidneys and surrounding soft tissue, with a positive correlation between OBR and halo size. Comparing different variants of scatter correction, reducing the maximum scatter fraction from the default value

Comparative Genomics as a Foundation for Evo-Devo Studies in Birds.

PubMed

Grayson, Phil; Sin, Simon Y W; Sackton, Timothy B; Edwards, Scott V

2017-01-01

Developmental genomics is a rapidly growing field, and high-quality genomes are a useful foundation for comparative developmental studies. A high-quality genome forms an essential reference onto which the data from numerous assays and experiments, including ChIP-seq, ATAC-seq, and RNA-seq, can be mapped. A genome also streamlines and simplifies the development of primers used to amplify putative regulatory regions for enhancer screens, cDNA probes for in situ hybridization, microRNAs (miRNAs) or short hairpin RNAs (shRNA) for RNA interference (RNAi) knockdowns, mRNAs for misexpression studies, and even guide RNAs (gRNAs) for CRISPR knockouts. Finally, much can be gleaned from comparative genomics alone, including the identification of highly conserved putative regulatory regions. This chapter provides an overview of laboratory and bioinformatics protocols for DNA extraction, library preparation, library quantification, and genome assembly, from fresh or frozen tissue to a draft avian genome. Generating a high-quality draft genome can provide a developmental research group with excellent resources for their study organism, opening the doors to many additional assays and experiments.

The immitigable nature of assembly bias: the impact of halo definition on assembly bias

NASA Astrophysics Data System (ADS)

Villarreal, Antonio S.; Zentner, Andrew R.; Mao, Yao-Yuan; Purcell, Chris W.; van den Bosch, Frank C.; Diemer, Benedikt; Lange, Johannes U.; Wang, Kuan; Campbell, Duncan

2017-11-01

Dark matter halo clustering depends not only on halo mass, but also on other properties such as concentration and shape. This phenomenon is known broadly as assembly bias. We explore the dependence of assembly bias on halo definition, parametrized by spherical overdensity parameter, Δ. We summarize the strength of concentration-, shape-, and spin-dependent halo clustering as a function of halo mass and halo definition. Concentration-dependent clustering depends strongly on mass at all Δ. For conventional halo definitions (Δ ∼ 200 - 600 m), concentration-dependent clustering at low mass is driven by a population of haloes that is altered through interactions with neighbouring haloes. Concentration-dependent clustering can be greatly reduced through a mass-dependent halo definition with Δ ∼ 20 - 40 m for haloes with M200 m ≲ 1012 h-1M⊙. Smaller Δ implies larger radii and mitigates assembly bias at low mass by subsuming altered, so-called backsplash haloes into now larger host haloes. At higher masses (M200 m ≳ 1013 h-1M⊙) larger overdensities, Δ ≳ 600 m, are necessary. Shape- and spin-dependent clustering are significant for all halo definitions that we explore and exhibit a relatively weaker mass dependence. Generally, both the strength and the sense of assembly bias depend on halo definition, varying significantly even among common definitions. We identify no halo definition that mitigates all manifestations of assembly bias. A halo definition that mitigates assembly bias based on one halo property (e.g. concentration) must be mass dependent. The halo definitions that best mitigate concentration-dependent halo clustering do not coincide with the expected average splashback radii at fixed halo mass.

Testing approximate predictions of displacements of cosmological dark matter halos

NASA Astrophysics Data System (ADS)

Munari, Emiliano; Monaco, Pierluigi; Koda, Jun; Kitaura, Francisco-Shu; Sefusatti, Emiliano; Borgani, Stefano

2017-07-01

We present a test to quantify how well some approximate methods, designed to reproduce the mildly non-linear evolution of perturbations, are able to reproduce the clustering of DM halos once the grouping of particles into halos is defined and kept fixed. The following methods have been considered: Lagrangian Perturbation Theory (LPT) up to third order, Truncated LPT, Augmented LPT, MUSCLE and COLA. The test runs as follows: halos are defined by applying a friends-of-friends (FoF) halo finder to the output of an N-body simulation. The approximate methods are then applied to the same initial conditions of the simulation, producing for all particles displacements from their starting position and velocities. The position and velocity of each halo are computed by averaging over the particles that belong to that halo, according to the FoF halo finder. This procedure allows us to perform a well-posed test of how clustering of the matter density and halo density fields are recovered, without asking to the approximate method an accurate reconstruction of halos. We have considered the results at z=0,0.5,1, and we have analysed power spectrum in real and redshift space, object-by-object difference in position and velocity, density Probability Distribution Function (PDF) and its moments, phase difference of Fourier modes. We find that higher LPT orders are generally able to better reproduce the clustering of halos, while little or no improvement is found for the matter density field when going to 2LPT and 3LPT. Augmentation provides some improvement when coupled with 2LPT, while its effect is limited when coupled with 3LPT. Little improvement is brought by MUSCLE with respect to Augmentation. The more expensive particle-mesh code COLA outperforms all LPT methods, and this is true even for mesh sizes as large as the inter-particle distance. This test sets an upper limit on the ability of these methods to reproduce the clustering of halos, for the cases when these objects are

What constitutes an Arabian Helicobacter pylori? Lessons from comparative genomics.

PubMed

Kumar, Narender; Albert, M John; Al Abkal, Hanan; Siddique, Iqbal; Ahmed, Niyaz

2017-02-01

Helicobacter pylori, the human gastric pathogen, causes a variety of gastric diseases ranging from mild gastritis to gastric cancer. While the studies on H. pylori are dominated by those based on either East Asian or Western strains, information regarding H. pylori strains prevalent in the Middle East remains scarce. Therefore, we carried out whole-genome sequencing and comparative analysis of three H. pylori strains isolated from three native Arab, Kuwaiti patients. H. pylori strains were sequenced using Illumina platform. The sequence reads were filtered and draft genomes were assembled and annotated. Various pathogenicity-associated regions and phages present within the genomes were identified. Phylogenetic analysis was carried out to determine the genetic relatedness of Kuwaiti strains to various lineages of H. pylori. The core genome content and virulence-related genes were analyzed to assess the pathogenic potential. The three genomes clustered along with HpEurope strains in the phylogenetic tree comprising various H. pylori lineages. A total of 1187 genes spread among various functional classes were identified in the core genome analysis. The three genomes possessed a complete cagPAI and also retained most of the known outer membrane proteins as well as virulence-related genes. The cagA gene in all three strains consisted of an AB-C type EPIYA motif. The comparative genomic analysis of Kuwaiti H. pylori strains revealed a European ancestry and a high pathogenic potential. © 2016 John Wiley & Sons Ltd.

Chemical Cartography. I. A Carbonicity Map of the Galactic Halo

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

Lee, Young Sun; Kim, Young Kwang; Beers, Timothy C.

We present the first map of carbonicity, [C/Fe], for the halo system of the Milky Way, based on a sample of over 100,000 main-sequence turnoff stars with available spectroscopy from the Sloan Digital Sky Survey. This map, which explores distances up to 15 kpc from the Sun, reveals clear evidence for the dual nature of the Galactic halo, based on the spatial distribution of stellar carbonicity. The metallicity distribution functions of stars in the inner- and outer-halo regions of the carbonicity map reproduce those previously argued to arise from contributions of the inner- and outer-halo populations, with peaks at [Fe/H]more » = −1.5 and −2.2, respectively. From consideration of the absolute carbon abundances for our sample, A (C), we also confirm that the carbon-enhanced metal-poor (CEMP) stars in the outer-halo region exhibit a higher frequency of CEMP-no stars (those with no overabundances of heavy neutron-capture elements) than of CEMP- s stars (those with strong overabundances of elements associated with the s -process), whereas the stars in the inner-halo region exhibit a higher frequency of CEMP- s stars. We argue that the contrast in the behavior of the CEMP-no and CEMP- s fractions in these regions arises from differences in the mass distributions of the mini-halos from which the stars of the inner- and outer-halo populations formed, which gives rise in turn to the observed dichotomy of the Galactic halo.« less

Hierarchical formation of dark matter halos and the free streaming scale

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

Ishiyama, Tomoaki, E-mail: ishiyama@ccs.tsukuba.ac.jp

2014-06-10

The smallest dark matter halos are formed first in the early universe. According to recent studies, the central density cusp is much steeper in these halos than in larger halos and scales as ρ∝r {sup –(1.5-1.3)}. We present the results of very large cosmological N-body simulations of the hierarchical formation and evolution of halos over a wide mass range, beginning from the formation of the smallest halos. We confirmed early studies that the inner density cusps are steeper in halos at the free streaming scale. The cusp slope gradually becomes shallower as the halo mass increases. The slope of halosmore » 50 times more massive than the smallest halo is approximately –1.3. No strong correlation exists between the inner slope and the collapse epoch. The cusp slope of halos above the free streaming scale seems to be reduced primarily due to major merger processes. The concentration, estimated at the present universe, is predicted to be 60-70, consistent with theoretical models and earlier simulations, and ruling out simple power law mass-concentration relations. Microhalos could still exist in the present universe with the same steep density profiles.« less

Unveiling the stellar halo with TGAS

NASA Astrophysics Data System (ADS)

Veljanoski, Jovan; Posti, L.; Helmi, A.; Breddels, M. A.

2018-04-01

The detailed study of the Galactic stellar halo may hold the key to unlocking the assembly history of the Milky Way. Here, we present a machine learning model for selecting metal poor stars from the TGAS catalogue using 5 dimensional phase-space information, coupled with optical and near-IR photometry. We characterise the degree of substructure in our halo sample in the Solar neighbourhood by measuring the velocity correlation function.

Biomechanics of halo-vest and dens screw fixation for type II odontoid fracture.

PubMed

Ivancic, Paul C; Beauchman, Naseem N; Mo, Fred; Lawrence, Brandon D

2009-03-01

An in vitro biomechanical study of halo-vest and odontoid screw fixation of Type II dens fracture. The objective were to determine upper cervical spine instability due to simulated dens fracture and investigate stability provided by the halo-vest and odontoid screw, applied individually and combined. Previous studies have evaluated posterior fixation techniques for stabilizing dens fracture. No previous biomechanical study has investigated the halo-vest and odontoid screw for stabilizing dens fracture. A biofidelic skull-neck-thorax model was used with 5 osteoligamentous whole cervical spine specimens. Three-dimensional flexibility tests were performed on the specimens while intact, following simulated dens fracture, and following application of the halo-vest alone, odontoid screw alone, and halo-vest and screw combined. Average total neutral zone and total ranges of motion at C0/1 and C1/2 were computed for each experimental condition and statistically compared with physiologic motion limits, obtained from the intact flexibility test. Significance was set at P < 0.05 with a trend toward significance at P < 0.1. Type II dens fracture caused trends toward increased sagittal neutral zone and lateral bending range of motion at C1/2. Spinal motions with the dens screw alone could not be differentiated from physiologic limits. Significant reductions in motion were observed at C0/1 and C1/2 in flexion-extension and axial rotation due to the halo-vest, applied individually or combined with the dens screw. At C1/2, the halo-vest combined with the dens screw generally allowed the smallest average percentages of intact motion: 3% in axial rotation, 17% in flexion-extension, and 18% in lateral bending. The present reduction in C1/2 motion observed, due to the halo-vest and dens screw combined is similar to previously reported immobilization provided by the polyaxial screw/rod system and transarticular screw fixation combined with wiring. The present biomechanical data may be

Implementation of a 3D halo neutral model in the TRANSP code and application to projected NSTX-U plasmas

NASA Astrophysics Data System (ADS)

Medley, S. S.; Liu, D.; Gorelenkova, M. V.; Heidbrink, W. W.; Stagner, L.

2016-02-01

A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a ‘beam-in-a-box’ model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components produce first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.

Implementation of a 3D halo neutral model in the TRANSP code and application to projected NSTX-U plasmas

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

Medley, S. S.; Liu, D.; Gorelenkova, M. V.

2016-01-12

A 3D halo neutral code developed at the Princeton Plasma Physics Laboratory and implemented for analysis using the TRANSP code is applied to projected National Spherical Torus eXperiment-Upgrade (NSTX-U plasmas). The legacy TRANSP code did not handle halo neutrals properly since they were distributed over the plasma volume rather than remaining in the vicinity of the neutral beam footprint as is actually the case. The 3D halo neutral code uses a 'beam-in-a-box' model that encompasses both injected beam neutrals and resulting halo neutrals. Upon deposition by charge exchange, a subset of the full, one-half and one-third beam energy components producemore » first generation halo neutrals that are tracked through successive generations until an ionization event occurs or the descendant halos exit the box. The 3D halo neutral model and neutral particle analyzer (NPA) simulator in the TRANSP code have been benchmarked with the Fast-Ion D-Alpha simulation (FIDAsim) code, which provides Monte Carlo simulations of beam neutral injection, attenuation, halo generation, halo spatial diffusion, and photoemission processes. When using the same atomic physics database, TRANSP and FIDAsim simulations achieve excellent agreement on the spatial profile and magnitude of beam and halo neutral densities and the NPA energy spectrum. The simulations show that the halo neutral density can be comparable to the beam neutral density. These halo neutrals can double the NPA flux, but they have minor effects on the NPA energy spectrum shape. The TRANSP and FIDAsim simulations also suggest that the magnitudes of beam and halo neutral densities are relatively sensitive to the choice of the atomic physics databases.« less

Cocoa/Cotton Comparative Genomics

USDA-ARS?s Scientific Manuscript database

With genome sequence from two members of the Malvaceae family recently made available, we are exploring syntenic relationships, gene content, and evolutionary trajectories between the cacao and cotton genomes. An assembly of cacao (Theobroma cacao) using Illumina and 454 sequence technology yielded ...

Comparative genome analysis of Basidiomycete fungi

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

Riley, Robert; Salamov, Asaf; Henrissat, Bernard

Fungi of the phylum Basidiomycota (basidiomycetes), make up some 37percent of the described fungi, and are important in forestry, agriculture, medicine, and bioenergy. This diverse phylum includes symbionts, pathogens, and saprotrophs including the majority of wood decaying and ectomycorrhizal species. To better understand the genetic diversity of this phylum we compared the genomes of 35 basidiomycetes including 6 newly sequenced genomes. These genomes span extremes of genome size, gene number, and repeat content. Analysis of core genes reveals that some 48percent of basidiomycete proteins are unique to the phylum with nearly half of those (22percent) found in only one organism.more » Correlations between lifestyle and certain gene families are evident. Phylogenetic patterns of plant biomass-degrading genes in Agaricomycotina suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wood decay. Based on phylogenetically-informed PCA analysis of wood decay genes, we predict that that Botryobasidium botryosum and Jaapia argillacea have properties similar to white rot species, although neither has typical ligninolytic class II fungal peroxidases (PODs). This prediction is supported by growth assays in which both fungi exhibit wood decay with white rot-like characteristics. Based on this, we suggest that the white/brown rot dichotomy may be inadequate to describe the full range of wood decaying fungi. Analysis of the rate of discovery of proteins with no or few homologs suggests the value of continued sequencing of basidiomycete fungi.« less

The segregation of baryons and dark matter during halo assembly

NASA Astrophysics Data System (ADS)

Liao, Shihong; Gao, Liang; Frenk, Carlos S.; Guo, Qi; Wang, Jie

2017-09-01

The standard galaxy formation theory assumes that baryons and dark matter are initially well mixed before becoming segregated due to radiative cooling. We use non-radiative hydrodynamical simulations to explicitly examine this assumption and find that baryons and dark matter can also be segregated due to different characteristics of gas and dark matter during the buildup of the halo. As a result, baryons in many haloes do not originate from the same Lagrangian region as the dark matter. When using the fraction of corresponding dark matter and gas particles in the initial conditions (the 'paired fraction') as a proxy of the dark matter and gas segregation strength of a halo, on average about 25 per cent of the baryonic and dark matter of the final halo are segregated in the initial conditions. This is at odds with the assumption of the standard galaxy formation model. A consequence of this effect is that the baryons and dark matter of the same halo initially experience different tidal torques and thus their angular momentum vectors are often misaligned. The degree of the misalignment is largely preserved during later halo assembly and can be understood with the tidal torque theory. The result challenges the precision of some semi-analytical approaches that utilize dark matter halo merger trees to infer properties of gas associated with dark matter haloes.

Comparative ruminant genomics highlights segmental duplication and mobile element insertion diversity

USDA-ARS?s Scientific Manuscript database

We have expanded upon a previously reported comparative genomics approach using a read-depth (JaRMs) and a hybrid read-pair, split-read (RAPTR-SV) copy number variation (CNV) detection method that uses read alignments to the cattle reference genome in order to identify species-specific genomic rearr...

Dust-Driven Halos on the Martian South Polar Residual CAP

NASA Astrophysics Data System (ADS)

Becerra, P.; Byrne, S.; Brown, A. J.

2013-12-01

The CO2 ice South Polar Residual Cap (SPRC) on Mars may be a sensitive indicator of inter-annual planetary climate variability. Imaging by HiRISE [1], and CTX [2] found that many scarps and pits in the 'Swiss cheese terrain' [3] of the SPRC exhibited a bright 'halo' around their edges. These halos appeared during Martian southern summer in Mars Year 28 (MY28, [4]), and have been observed in only one of eight mars years for which observations at high enough resolution exist. We hypothesize that the formation of these features is linked to the late-summer global dust storm of MY28 and report on observations and formation models. We surveyed HiRISE, CTX, and CRISM [5] data to constrain the optical properties and composition of the halos, as well as their time of appearance and location within the SPRC. The halos appeared throughout most of the surface area of the SPRC between Ls 280° and 330° in MY28. The widest portions of the halos occurred adjacent to north-facing walls, and the brightest parts adjacent to sun-facing walls, which points to a connection between insolation and halo appearance. CRISM spectral products rule out the presence of water ice as a factor in the halos' appearance. These data also imply larger CO2 ice grain sizes where the bright halos were seen, which are normally associated with lower, rather than higher, albedos [6]. Thus, we also ruled out CO2 ice grain size differences as the main cause for the halos. The remaining possibility is that the halos appeared due to differences in dust content between the terrain adjacent to the pit walls and the surrounding ice. To investigate this we made a Hapke [7] surface reflectance model in which the CO2 ice grain size, dust volumetric content and dust particle size were free parameters. We used the HiRISE and CRISM bandpass coefficients to simulate HiRISE I/F values and CRISM spectra, and attempted to match the HiRISE RED I/F, HiRISE BG/RED color ratio, and the CRISM 1.43 μm band depths. A self

Dark Matter Halos with VIRUS-P

NASA Astrophysics Data System (ADS)

Murphy, Jeremy; Gebhardt, K.

2010-05-01

We present new, two-dimensional stellar kinematic data on several of the most massive galaxies in the local universe. These data were taken with the integral field spectrograph, VIRUS-P, and extend to unprecedented radial distances. Once robust stellar kinematics are in hand, we run orbit-based axisymmetric dynamical models in order to constrain the stellar mass-to-light ratio and dark matter halo parameters. We have run a large set of dynamical models on the second rank galaxy in the Virgo cluster, M87, and find clear evidence for a massive dark matter halo. The two-dimensional stellar kinematics for several of our other targets, all first and second rank galaxies, are also presented. Dark matter halos are known to dominate the mass profile of elliptical galaxies somewhere between one to two effective radii, yet due to the low surface brightness at these radial distances, determining stellar dynamics is technologically challenging. To overcome this, constraints on the dark matter halo are often made with planetary nebulae or globular clusters at large radii. However, as results from different groups have returned contradictory results, it remains unclear whether different dynamical tracers always follow the stellar kinematics. Due to VIRUS-P's large field of view and on-sky fiber diameter, we are able to determine stellar kinematics at radial distances that overlap with other dynamical tracers. Understanding what the dynamics of stars, planetary nebula and globular clusters tell us about both the extent of the dark matter halo profile and the formation histories of the largest elliptical galaxies is a primary science driver for this work.

VizieR Online Data Catalog: The SEGUE K giant survey. III. Galactic halo (Janesh+, 2016)

NASA Astrophysics Data System (ADS)

Janesh, W.; Morrison, H. L.; Ma, Z.; Rockosi, C.; Starkenburg, E.; Xue, X. X.; Rix, H.-W.; Harding, P.; Beers, T. C.; Johnson, J.; Lee, Y. S.; Schneider, D. P.

2016-03-01

We statistically quantify the amount of substructure in the Milky Way stellar halo using a sample of 4568 halo K giant stars at Galactocentric distances ranging over 5-125kpc. These stars have been selected photometrically and confirmed spectroscopically as K giants from the Sloan Digital Sky Survey's Sloan Extension for Galactic Understanding and Exploration (SEGUE) project. Using a position-velocity clustering estimator (the 4distance) and a model of a smooth stellar halo, we quantify the amount of substructure in the halo, divided by distance and metallicity. Overall, we find that the halo as a whole is highly structured. We also confirm earlier work using blue horizontal branch (BHB) stars which showed that there is an increasing amount of substructure with increasing Galactocentric radius, and additionally find that the amount of substructure in the halo increases with increasing metallicity. Comparing to resampled BHB stars, we find that K giants and BHBs have similar amounts of substructure over equivalent ranges of Galactocentric radius. Using a friends-of-friends algorithm to identify members of individual groups, we find that a large fraction (~33%) of grouped stars are associated with Sgr, and identify stars belonging to other halo star streams: the Orphan Stream, the Cetus Polar Stream, and others, including previously unknown substructures. A large fraction of sample K giants (more than 50%) are not grouped into any substructure. We find also that the Sgr stream strongly dominates groups in the outer halo for all except the most metal-poor stars, and suggest that this is the source of the increase of substructure with Galactocentric radius and metallicity. (2 data files).

An accurate halo model for fitting non-linear cosmological power spectra and baryonic feedback models

NASA Astrophysics Data System (ADS)

Mead, A. J.; Peacock, J. A.; Heymans, C.; Joudaki, S.; Heavens, A. F.

2015-12-01

We present an optimized variant of the halo model, designed to produce accurate matter power spectra well into the non-linear regime for a wide range of cosmological models. To do this, we introduce physically motivated free parameters into the halo-model formalism and fit these to data from high-resolution N-body simulations. For a variety of Λ cold dark matter (ΛCDM) and wCDM models, the halo-model power is accurate to ≃ 5 per cent for k ≤ 10h Mpc-1 and z ≤ 2. An advantage of our new halo model is that it can be adapted to account for the effects of baryonic feedback on the power spectrum. We demonstrate this by fitting the halo model to power spectra from the OWLS (OverWhelmingly Large Simulations) hydrodynamical simulation suite via parameters that govern halo internal structure. We are able to fit all feedback models investigated at the 5 per cent level using only two free parameters, and we place limits on the range of these halo parameters for feedback models investigated by the OWLS simulations. Accurate predictions to high k are vital for weak-lensing surveys, and these halo parameters could be considered nuisance parameters to marginalize over in future analyses to mitigate uncertainty regarding the details of feedback. Finally, we investigate how lensing observables predicted by our model compare to those from simulations and from HALOFIT for a range of k-cuts and feedback models and quantify the angular scales at which these effects become important. Code to calculate power spectra from the model presented in this paper can be found at https://github.com/alexander-mead/hmcode.

Cosmic stellar relics in the Galactic halo

NASA Astrophysics Data System (ADS)

Salvadori, Stefania; Schneider, Raffaella; Ferrara, Andrea

2007-10-01

We study the stellar population history and chemical evolution of the Milky Way (MW) in a hierarchical Λ cold dark matter model for structure formation. Using a Monte Carlo method based on the semi-analytical extended Press & Schechter formalism, we develop a new code GALAXY MERGER TREE AND EVOLUTION (GAMETE) to reconstruct the merger tree of the Galaxy and follow the evolution of gas and stars along the hierarchical tree. Our approach allows us to compare the observational properties of the MW with model results, exploring different properties of primordial stars, such as their initial mass function and the critical metallicity for low-mass star formation, Zcr. In particular, by matching our predictions to the metallicity distribution function (MDF) of metal-poor stars in the Galactic halo we find that: (i) a strong supernova (SN) feedback is required to reproduce the observed properties of the MW; (ii) stars with [Fe/H] < -2.5 form in haloes accreting Galactic medium (GM) enriched by earlier SN explosions; (iii) the fiducial model (Zcr = 10-4Zsolar, mPopIII = 200 Msolar) provides an overall good fit to the MDF, but cannot account for the two hyper-metal-poor (HMP) stars with [Fe/H] < -5 the latter can be accommodated if Zcr <= 10-6 Zsolar but such model overpopulates the `metallicity desert', that is, the range -5.3 < [Fe/H] < -4 in which no stars have been detected; (iv) the current non-detection of metal-free stars robustly constrains either Zcr > 0 or the masses of the first stars mPopIII > 0.9 Msolar (v) the statistical impact of truly second-generation stars, that is, stars forming out of gas polluted only by metal-free stars, is negligible in current samples; and (vi) independent of Zcr, 60 per cent of metals in the GM are ejected through winds by haloes with masses M < 6 × 109 Msolar, thus showing that low-mass haloes are the dominant population contributing to cosmic metal enrichment. We discuss the limitations of our study and comparison with previous

Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure

PubMed Central

Coyne, Robert S; Thiagarajan, Mathangi; Jones, Kristie M; Wortman, Jennifer R; Tallon, Luke J; Haas, Brian J; Cassidy-Hanley, Donna M; Wiley, Emily A; Smith, Joshua J; Collins, Kathleen; Lee, Suzanne R; Couvillion, Mary T; Liu, Yifan; Garg, Jyoti; Pearlman, Ronald E; Hamilton, Eileen P; Orias, Eduardo; Eisen, Jonathan A; Methé, Barbara A

2008-01-01

Background Tetrahymena thermophila, a widely studied model for cellular and molecular biology, is a binucleated single-celled organism with a germline micronucleus (MIC) and somatic macronucleus (MAC). The recent draft MAC genome assembly revealed low sequence repetitiveness, a result of the epigenetic removal of invasive DNA elements found only in the MIC genome. Such low repetitiveness makes complete closure of the MAC genome a feasible goal, which to achieve would require standard closure methods as well as removal of minor MIC contamination of the MAC genome assembly. Highly accurate preliminary annotation of Tetrahymena's coding potential was hindered by the lack of both comparative genomic sequence information from close relatives and significant amounts of cDNA evidence, thus limiting the value of the genomic information and also leaving unanswered certain questions, such as the frequency of alternative splicing. Results We addressed the problem of MIC contamination using comparative genomic hybridization with purified MIC and MAC DNA probes against a whole genome oligonucleotide microarray, allowing the identification of 763 genome scaffolds likely to contain MIC-limited DNA sequences. We also employed standard genome closure methods to essentially finish over 60% of the MAC genome. For the improvement of annotation, we have sequenced and analyzed over 60,000 verified EST reads from a variety of cellular growth and development conditions. Using this EST evidence, a combination of automated and manual reannotation efforts led to updates that affect 16% of the current protein-coding gene models. By comparing EST abundance, many genes showing apparent differential expression between these conditions were identified. Rare instances of alternative splicing and uses of the non-standard amino acid selenocysteine were also identified. Conclusion We report here significant progress in genome closure and reannotation of Tetrahymena thermophila. Our experience to date

The clustering of QSOs and the dark matter halos that host them

NASA Astrophysics Data System (ADS)

Zhao, Dong-Yao; Yan, Chang-Shuo; Lu, Youjun

2013-10-01

The spatial clustering of QSOs is an important measurable quantity which can be used to infer the properties of dark matter halos that host them. We construct a simple QSO model to explain the linear bias of QSOs measured by recent observations and explore the properties of dark matter halos that host a QSO. We assume that major mergers of dark matter halos can lead to the triggering of QSO phenomena, and the evolution of luminosity for a QSO generally shows two accretion phases, i.e., initially having a constant Eddington ratio due to the self-regulation of the accretion process when supply is sufficient, and then declining in rate with time as a power law due to either diminished supply or long term disk evolution. Using a Markov Chain Monte Carlo method, the model parameters are constrained by fitting the observationally determined QSO luminosity functions (LFs) in the hard X-ray and in the optical band simultaneously. Adopting the model parameters that best fit the QSO LFs, the linear bias of QSOs can be predicted and then compared with the observational measurements by accounting for various selection effects in different QSO surveys. We find that the latest measurements of the linear bias of QSOs from both the SDSS and BOSS QSO surveys can be well reproduced. The typical mass of SDSS QSOs at redshift 1.5 < z < 4.5 is ~ (3 - 6) × 1012 h-1 Msolar and the typical mass of BOSS QSOs at z ~ 2.4 is ~ 2 × 1012 h-1 Msolar. For relatively faint QSOs, the mass distribution of their host dark matter halos is wider than that of bright QSOs because faint QSOs can be hosted in both big halos and smaller halos, but bright QSOs are only hosted in big halos, which is part of the reason for the predicted weak dependence of the linear biases on the QSO luminosity.

Dissipative dark matter halos: The steady state solution

NASA Astrophysics Data System (ADS)

Foot, R.

2018-02-01

Dissipative dark matter, where dark matter particle properties closely resemble familiar baryonic matter, is considered. Mirror dark matter, which arises from an isomorphic hidden sector, is a specific and theoretically constrained scenario. Other possibilities include models with more generic hidden sectors that contain massless dark photons [unbroken U (1 ) gauge interactions]. Such dark matter not only features dissipative cooling processes but also is assumed to have nontrivial heating sourced by ordinary supernovae (facilitated by the kinetic mixing interaction). The dynamics of dissipative dark matter halos around rotationally supported galaxies, influenced by heating as well as cooling processes, can be modeled by fluid equations. For a sufficiently isolated galaxy with a stable star formation rate, the dissipative dark matter halos are expected to evolve to a steady state configuration which is in hydrostatic equilibrium and where heating and cooling rates locally balance. Here, we take into account the major cooling and heating processes, and numerically solve for the steady state solution under the assumptions of spherical symmetry, negligible dark magnetic fields, and that supernova sourced energy is transported to the halo via dark radiation. For the parameters considered, and assumptions made, we were unable to find a physically realistic solution for the constrained case of mirror dark matter halos. Halo cooling generally exceeds heating at realistic halo mass densities. This problem can be rectified in more generic dissipative dark matter models, and we discuss a specific example in some detail.

Stellar-to-halo mass relation of cluster galaxies

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

Niemiec, Anna; Jullo, Eric; Limousin, Marceau

In the formation of galaxy groups and clusters, the dark matter haloes containing satellite galaxies are expected to be tidally stripped in gravitational interactions with the host. We use galaxy-galaxy weak lensing to measure the average mass of dark matter haloes of satellite galaxies as a function of projected distance to the centre of the host, since stripping is expected to be greater for satellites closer to the centre of the cluster. We further classify the satellites according to their stellar mass: assuming that the stellar component of the galaxy is less disrupted by tidal stripping, stellar mass can bemore » used as a proxy of the infall mass. We study the stellar to halo mass relation of satellites as a function of the cluster-centric distance to measure tidal stripping. We use the shear catalogues of the DES science veri cation archive, the CFHTLenS and the CFHT Stripe 82 surveys, and we select satellites from the redMaPPer catalogue of clusters. For galaxies located in the outskirts of clusters, we nd a stellar to halo mass relation in good agreement with the theoretical expectations from Moster, Naab & White (2013) for central galaxies. In the centre of the cluster, we nd that this relation is shifted to smaller halo mass for a given stellar mass. We interpret this nding as further evidence for tidal stripping of dark matter haloes in high density environments.« less

Stellar-to-halo mass relation of cluster galaxies

DOE PAGES

Niemiec, Anna; Jullo, Eric; Limousin, Marceau; ...

2017-07-04

In the formation of galaxy groups and clusters, the dark matter haloes containing satellite galaxies are expected to be tidally stripped in gravitational interactions with the host. We use galaxy-galaxy weak lensing to measure the average mass of dark matter haloes of satellite galaxies as a function of projected distance to the centre of the host, since stripping is expected to be greater for satellites closer to the centre of the cluster. We further classify the satellites according to their stellar mass: assuming that the stellar component of the galaxy is less disrupted by tidal stripping, stellar mass can bemore » used as a proxy of the infall mass. We study the stellar to halo mass relation of satellites as a function of the cluster-centric distance to measure tidal stripping. We use the shear catalogues of the DES science veri cation archive, the CFHTLenS and the CFHT Stripe 82 surveys, and we select satellites from the redMaPPer catalogue of clusters. For galaxies located in the outskirts of clusters, we nd a stellar to halo mass relation in good agreement with the theoretical expectations from Moster, Naab & White (2013) for central galaxies. In the centre of the cluster, we nd that this relation is shifted to smaller halo mass for a given stellar mass. We interpret this nding as further evidence for tidal stripping of dark matter haloes in high density environments.« less

Halo abundance and assembly history with extreme-axion wave dark matter at z ≥ 4

NASA Astrophysics Data System (ADS)

Schive, Hsi-Yu; Chiueh, Tzihong

2018-01-01

Wave dark matter (ψDM) composed of extremely light bosons (mψ ˜ 10 - 22 eV), with quantum pressure suppressing structures below a kpc-scale de Broglie wavelength, has become a viable dark matter candidate. Compared to the conventional free-particle ψDM (FPψDM), the extreme-axion ψDM model (EAψDM) proposed by Zhang & Chiueh features a larger cut-off wavenumber and a broad spectral bump in the matter transfer function. Here, we conduct cosmological simulations to compare the halo abundances and assembly histories at z = 4-11 between three different scenarios: FPψDM, EAψDM and cold dark matter (CDM). We show that EAψDM produces significantly more abundant low-mass haloes than FPψDM with the same mψ, and therefore could alleviate the tension in mψ required by the Lyα forest data and by the kpc-scale dwarf galaxy cores. We also find that, compared to the CDM counterparts, massive EAψDM haloes are, on average, 3-4 times more massive at z = 10-11 due to their earlier formation, undergo a slower mass accretion at 7 ≲ z ≲ 11, and then show a rapidly rising major merger rate exceeding CDM by ˜ 50 per cent at 4 ≲ z ≲ 7. This fact suggests that EAψDM haloes may exhibit more prominent starbursts at z ≲ 7.

The X-ray Halo of GX5-1

NASA Technical Reports Server (NTRS)

Smith, Randall K.; Dame, T. M.; Costantini, Elisa; Predehl, Peter

2006-01-01

Using Chandra observations we have measured the energy-resolved dust-scattered X-ray halo around the low-mass X-ray binary GX5-1, detecting for the first time multiply scattered X-rays from interstellar dust. % e compared the observed X-ray halo at various energies to predictions from a range of dust models. These fits used both smoothly-distributed dust as well as dust in clumped clouds, with CO and 21 cm observations helping to determine the position of the clouds along the line of sight. We found that the BARE-GR-B model of Zubko, Dwek & Arendt (2004) generally led to the best results, although inadequacies in both the overall model and the data limit our conclusions. We did find that the composite dust models of Zubko, Dwek & Arendt (2004), especially the "no carbon" models, gave uniformly poor results. Although models using cloud positions and densities derived naively from CO and 21 cm data gave generally poor results, plausible adjustments to the distance of the largest cloud and the mass of a cloud in the expanding 3 kpc Arm lead to significantly improved fits. We suggest that combining X-ray halo, CO, and 21 cm observations will be a fruitful method to improve our understanding of both the gas and dust phases of the interstellar medium.

Comparative Bacterial Proteomics: Analysis of the Core Genome Concept

PubMed Central

Callister, Stephen J.; McCue, Lee Ann; Turse, Joshua E.; Monroe, Matthew E.; Auberry, Kenneth J.; Smith, Richard D.; Adkins, Joshua N.; Lipton, Mary S.

2008-01-01

While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits. PMID:18253490

Genome profiling of ovarian adenocarcinomas using pangenomic BACs microarray comparative genomic hybridization

PubMed Central

Caserta, Donatella; Benkhalifa, Moncef; Baldi, Marina; Fiorentino, Francesco; Qumsiyeh, Mazin; Moscarini, Massimo

2008-01-01

Background Routine cytogenetic investigations for ovarian cancers are limited by culture failure and poor growth of cancer cells compared to normal cells. Fluorescence in situ Hybridization (FISH) application or classical comparative genome hybridization techniques are also have their own limitations in detecting genome imbalance especially for small changes that are not known ahead of time and for which FISH probes could not be thus designed. Methods We applied microarray comparative genomic hybridization (A-CGH) using one mega base BAC arrays to investigate chromosomal disorders in ovarian adenocarcinoma in patients with familial history. Results Our data on 10 cases of ovarian cancer revealed losses of 6q (4 cases mainly mosaic loss), 9p (4 cases), 10q (3 cases), 21q (3 cases), 22q (4 cases) with association to a monosomy X and gains of 8q and 9q (occurring together in 8 cases) and gain of 12p. There were other abnormalities such as loss of 17p that were noted in two profiles of the studied cases. Total or mosaic segmental gain of 2p, 3q, 4q, 7q and 13q were also observed. Seven of 10 patients were investigated by FISH to control array CGH results. The FISH data showed a concordance between the 2 methods. Conclusion The data suggest that A-CGH detects unique and common abnormalities with certain exceptions such as tetraploidy and balanced translocation, which may lead to understanding progression of genetic changes as well as aid in early diagnosis and have an impact on therapy and prognosis. PMID:18492273

Comparative genomics of the Bifidobacterium breve taxon.

PubMed

Bottacini, Francesca; O'Connell Motherway, Mary; Kuczynski, Justin; O'Connell, Kerry Joan; Serafini, Fausta; Duranti, Sabrina; Milani, Christian; Turroni, Francesca; Lugli, Gabriele Andrea; Zomer, Aldert; Zhurina, Daria; Riedel, Christian; Ventura, Marco; van Sinderen, Douwe

2014-03-01

Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina. In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol. Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.

Stellar Velocity Dispersion: Linking Quiescent Galaxies to Their Dark Matter Halos

NASA Astrophysics Data System (ADS)

Zahid, H. Jabran; Sohn, Jubee; Geller, Margaret J.

2018-06-01

We analyze the Illustris-1 hydrodynamical cosmological simulation to explore the stellar velocity dispersion of quiescent galaxies as an observational probe of dark matter halo velocity dispersion and mass. Stellar velocity dispersion is proportional to dark matter halo velocity dispersion for both central and satellite galaxies. The dark matter halos of central galaxies are in virial equilibrium and thus the stellar velocity dispersion is also proportional to dark matter halo mass. This proportionality holds even when a line-of-sight aperture dispersion is calculated in analogy to observations. In contrast, at a given stellar velocity dispersion, the dark matter halo mass of satellite galaxies is smaller than virial equilibrium expectations. This deviation from virial equilibrium probably results from tidal stripping of the outer dark matter halo. Stellar velocity dispersion appears insensitive to tidal effects and thus reflects the correlation between stellar velocity dispersion and dark matter halo mass prior to infall. There is a tight relation (≲0.2 dex scatter) between line-of-sight aperture stellar velocity dispersion and dark matter halo mass suggesting that the dark matter halo mass may be estimated from the measured stellar velocity dispersion for both central and satellite galaxies. We evaluate the impact of treating all objects as central galaxies if the relation we derive is applied to a statistical ensemble. A large fraction (≳2/3) of massive quiescent galaxies are central galaxies and systematic uncertainty in the inferred dark matter halo mass is ≲0.1 dex thus simplifying application of the simulation results to currently available observations.

New halo formation mechanism at the KEK compact energy recovery linac

NASA Astrophysics Data System (ADS)

Tanaka, Olga; Nakamura, Norio; Shimada, Miho; Miyajima, Tsukasa; Ueda, Akira; Obina, Takashi; Takai, Ryota

2018-02-01

The beam halo mitigation is a very important challenge for reliable and safe operation of a high-energy machine. A systematic beam halo study was conducted at the KEK compact energy recovery linac (cERL) since non-negligible beam loss was observed in the recirculation loop during a common operation. We found that the beam loss can be avoided by making use of the collimation system. Beam halo measurements have demonstrated the presence of vertical beam halos at multiple locations in the beam line (except the region near the electron gun). Based on these observations, we made a conjecture that the transverse beam halo is attributed to the longitudinal bunch tail arising at the photocathode. The transfer of particles from the longitudinal space to a transverse halo may have been observed and studied in other machines, considering nonlinear effects as their causes. However, our study demonstrates a new unique halo formation mechanism, in which a transverse beam halo can be generated by a longitudinal bunch tail due to transverse rf kicks from the accelerating (monopole) fields of the radio-frequency cavities. This halo formation occurs when nonrelativistic particles enter the cavities with a transverse offset, even if neither nonlinear optics nor nonlinear beam effects are present. A careful realignment of the injector system will mitigate the present halo. Another possible cure is to reduce the bunch tails by changing the photocathode material from the present GaAs to a multi-alkali that is known to have a shorter longitudinal tail.

Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

PubMed

Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2014-06-01

To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

The genomes and comparative genomics of Lactobacillus delbrueckii phages.

PubMed

Riipinen, Katja-Anneli; Forsman, Päivi; Alatossava, Tapani

2011-07-01

Lactobacillus delbrueckii phages are a great source of genetic diversity. Here, the genome sequences of Lb. delbrueckii phages LL-Ku, c5 and JCL1032 were analyzed in detail, and the genetic diversity of Lb. delbrueckii phages belonging to different taxonomic groups was explored. The lytic isometric group b phages LL-Ku (31,080 bp) and c5 (31,841 bp) showed a minimum nucleotide sequence identity of 90% over about three-fourths of their genomes. The genomic locations of their lysis modules were unique, and the genomes featured several putative overlapping transcription units of genes. LL-Ku and c5 virions displayed peptidoglycan hydrolytic activity associated with a ~36-kDa protein similar in size to the endolysin. Unexpectedly, the 49,433-bp genome of the prolate phage JCL1032 (temperate, group c) revealed a conserved gene order within its structural genes. Lb. delbrueckii phages representing groups a (a phage LL-H), b and c possessed only limited protein sequence homology. Genomic comparison of LL-Ku and c5 suggested that diversification of Lb. delbrueckii phages is mainly due to insertions, deletions and recombination. For the first time, the complete genome sequences of group b and c Lb. delbrueckii phages are reported.

Comparative genomics of 9 novel Paenibacillus larvae bacteriophages

PubMed Central

Stamereilers, Casey; LeBlanc, Lucy; Yost, Diane; Amy, Penny S.; Tsourkas, Philippos K.

2016-01-01

ABSTRACT American Foulbrood Disease, caused by the bacterium Paenibacillus larvae, is one of the most destructive diseases of the honeybee, Apis mellifera. Our group recently published the sequences of 9 new phages with the ability to infect and lyse P. larvae. Here, we characterize the genomes of these P. larvae phages, compare them to each other and to other sequenced P. larvae phages, and putatively identify protein function. The phage genomes are 38–45 kb in size and contain 68–86 genes, most of which appear to be unique to P. larvae phages. We classify P. larvae phages into 2 main clusters and one singleton based on nucleotide sequence identity. Three of the new phages show sequence similarity to other sequenced P. larvae phages, while the remaining 6 do not. We identified functions for roughly half of the P. larvae phage proteins, including structural, assembly, host lysis, DNA replication/metabolism, regulatory, and host-related functions. Structural and assembly proteins are highly conserved among our phages and are located at the start of the genome. DNA replication/metabolism, regulatory, and host-related proteins are located in the middle and end of the genome, and are not conserved, with many of these genes found in some of our phages but not others. All nine phages code for a conserved N-acetylmuramoyl-L-alanine amidase. Comparative analysis showed the phages use the “cohesive ends with 3′ overhang” DNA packaging strategy. This work is the first in-depth study of P. larvae phage genomics, and serves as a marker for future work in this area. PMID:27738559

Halo Profiles and the Concentration–Mass Relation for a ΛCDM Universe

NASA Astrophysics Data System (ADS)

Child, Hillary L.; Habib, Salman; Heitmann, Katrin; Frontiere, Nicholas; Finkel, Hal; Pope, Adrian; Morozov, Vitali

2018-05-01

Profiles of dark matter-dominated halos at the group and cluster scales play an important role in modern cosmology. Using results from two very large cosmological N-body simulations, which increase the available volume at their mass resolution by roughly two orders of magnitude, we robustly determine the halo concentration–mass (c‑M) relation over a wide range of masses, employing multiple methods of concentration measurement. We characterize individual halo profiles, as well as stacked profiles, relevant for galaxy–galaxy lensing and next-generation cluster surveys; the redshift range covered is 0 ≤ z ≤ 4, with a minimum halo mass of M 200c ∼ 2 × 1011 M ⊙. Despite the complexity of a proper description of a halo (environmental effects, merger history, nonsphericity, relaxation state), when the mass is scaled by the nonlinear mass scale M ⋆(z), we find that a simple non-power-law form for the c–M/M ⋆ relation provides an excellent description of our simulation results across eight decades in M/M ⋆ and for 0 ≤ z ≤ 4. Over the mass range covered, the c–M relation has two asymptotic forms: an approximate power law below a mass threshold M/M ⋆ ∼ 500–1000, transitioning to a constant value, c 0 ∼ 3 at higher masses. The relaxed halo fraction decreases with mass, transitioning to a constant value of ∼0.5 above the same mass threshold. We compare Navarro–Frenk–White (NFW) and Einasto fits to stacked profiles in narrow mass bins at different redshifts; as expected, the Einasto profile provides a better description of the simulation results. At cluster scales at low redshift, however, both NFW and Einasto profiles are in very good agreement with the simulation results, consistent with recent weak lensing observations.

Testing approximate predictions of displacements of cosmological dark matter halos

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

Munari, Emiliano; Monaco, Pierluigi; Borgani, Stefano

We present a test to quantify how well some approximate methods, designed to reproduce the mildly non-linear evolution of perturbations, are able to reproduce the clustering of DM halos once the grouping of particles into halos is defined and kept fixed. The following methods have been considered: Lagrangian Perturbation Theory (LPT) up to third order, Truncated LPT, Augmented LPT, MUSCLE and COLA. The test runs as follows: halos are defined by applying a friends-of-friends (FoF) halo finder to the output of an N-body simulation. The approximate methods are then applied to the same initial conditions of the simulation, producing formore » all particles displacements from their starting position and velocities. The position and velocity of each halo are computed by averaging over the particles that belong to that halo, according to the FoF halo finder. This procedure allows us to perform a well-posed test of how clustering of the matter density and halo density fields are recovered, without asking to the approximate method an accurate reconstruction of halos. We have considered the results at z =0,0.5,1, and we have analysed power spectrum in real and redshift space, object-by-object difference in position and velocity, density Probability Distribution Function (PDF) and its moments, phase difference of Fourier modes. We find that higher LPT orders are generally able to better reproduce the clustering of halos, while little or no improvement is found for the matter density field when going to 2LPT and 3LPT. Augmentation provides some improvement when coupled with 2LPT, while its effect is limited when coupled with 3LPT. Little improvement is brought by MUSCLE with respect to Augmentation. The more expensive particle-mesh code COLA outperforms all LPT methods, and this is true even for mesh sizes as large as the inter-particle distance. This test sets an upper limit on the ability of these methods to reproduce the clustering of halos, for the cases when these

Revisiting Scaling Relations for Giant Radio Halos in Galaxy Clusters

NASA Technical Reports Server (NTRS)

Cassano, R.; Ettori, S.; Brunetti, G.; Giacintucci, S.; Pratt, G. W.; Venturi, T.; Kale, R.; Dolag, K.; Markevitch, Maxim L.

2013-01-01

Many galaxy clusters host megaparsec-scale radio halos, generated by ultrarelativistic electrons in the magnetized intracluster medium. Correlations between the synchrotron power of radio halos and the thermal properties of the hosting clusters were established in the last decade, including the connection between the presence of a halo and cluster mergers. The X-ray luminosity and redshift-limited Extended GMRT Radio Halo Survey provides a rich and unique dataset for statistical studies of the halos. We uniformly analyze the radio and X-ray data for the GMRT cluster sample, and use the new Planck Sunyaev-Zel'dovich (SZ) catalog to revisit the correlations between the power of radio halos and the thermal properties of galaxy clusters. We find that the radio power at 1.4 GHz scales with the cluster X-ray (0.1-2.4 keV) luminosity computed within R(sub 500) as P(sub 1.4) approx. L(2.1+/-0.2) - 500). Our bigger and more homogenous sample confirms that the X-ray luminous (L(sub 500) > 5 × 10(exp 44) erg/s)) clusters branch into two populations-radio halos lie on the correlation, while clusters without radio halos have their radio upper limits well below that correlation. This bimodality remains if we excise cool cores from the X-ray luminosities. We also find that P(sub 1.4) scales with the cluster integrated SZ signal within R(sub 500), measured by Planck, as P(sub 1.4) approx. Y(2.05+/-0.28) - 500), in line with previous findings. However, contrary to previous studies that were limited by incompleteness and small sample size, we find that "SZ-luminous" Y(sub 500) > 6×10(exp -5) Mpc(exp 2) clusters show a bimodal behavior for the presence of radio halos, similar to that in the radio-X-ray diagram. Bimodality of both correlations can be traced to clusters dynamics, with radio halos found exclusively in merging clusters. These results confirm the key role of mergers for the origin of giant radio halos, suggesting that they trigger the relativistic particle acceleration.

Galaxy halo formation in the absence of violent relaxation and a universal density profile of the halo center

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

Baushev, A. N., E-mail: baushev@gmail.com; Institut für Physik und Astronomie, Universität Potsdam, D-14476 Potsdam-Golm

2014-05-01

While N-body simulations testify to a cuspy profile of the central region of dark matter halos, observations favor a shallow, cored density profile of the central region of at least some spiral galaxies and dwarf spheroidals. We show that a central profile, very close to the observed one, inevitably forms in the center of dark matter halos if we make a supposition about a moderate energy relaxation of the system during the halo formation. If we assume the energy exchange between dark matter particles during the halo collapse is not too intensive, the profile is universal: it depends almost notmore » at all on the properties of the initial perturbation and is very akin, but not identical, to the Einasto profile with a small Einasto index n ∼ 0.5. We estimate the size of the 'central core' of the distribution, i.e., the extent of the very central region with a respectively gentle profile, and show that the cusp formation is unlikely, even if the dark matter is cold. The obtained profile is in good agreement with observational data for at least some types of galaxies but clearly disagrees with N-body simulations.« less

Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation.

PubMed

Sharma, Virag; Hiller, Michael

2017-08-21

Genome alignments provide a powerful basis to transfer gene annotations from a well-annotated reference genome to many other aligned genomes. The completeness of these annotations crucially depends on the sensitivity of the underlying genome alignment. Here, we investigated the impact of the genome alignment parameters and found that parameters with a higher sensitivity allow the detection of thousands of novel alignments between orthologous exons that have been missed before. In particular, comparisons between species separated by an evolutionary distance of >0.75 substitutions per neutral site, like human and other non-placental vertebrates, benefit from increased sensitivity. To systematically test if increased sensitivity improves comparative gene annotations, we built a multiple alignment of 144 vertebrate genomes and used this alignment to map human genes to the other 143 vertebrates with CESAR. We found that higher alignment sensitivity substantially improves the completeness of comparative gene annotations by adding on average 2382 and 7440 novel exons and 117 and 317 novel genes for mammalian and non-mammalian species, respectively. Our results suggest a more sensitive alignment strategy that should generally be used for genome alignments between distantly-related species. Our 144-vertebrate genome alignment and the comparative gene annotations (https://bds.mpi-cbg.de/hillerlab/144VertebrateAlignment_CESAR/) are a valuable resource for comparative genomics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Comparative genomics of Enterococcus faecalis from healthy Norwegian infants

PubMed Central

Solheim, Margrete; Aakra, Ågot; Snipen, Lars G; Brede, Dag A; Nes, Ingolf F

2009-01-01

Background Enterococcus faecalis, traditionally considered a harmless commensal of the intestinal tract, is now ranked among the leading causes of nosocomial infections. In an attempt to gain insight into the genetic make-up of commensal E. faecalis, we have studied genomic variation in a collection of community-derived E. faecalis isolated from the feces of Norwegian infants. Results The E. faecalis isolates were first sequence typed by multilocus sequence typing (MLST) and characterized with respect to antibiotic resistance and properties associated with virulence. A subset of the isolates was compared to the vancomycin resistant strain E. faecalis V583 (V583) by whole genome microarray comparison (comparative genomic hybridization (CGH)). Several of the putative enterococcal virulence factors were found to be highly prevalent among the commensal baby isolates. The genomic variation as observed by CGH was less between isolates displaying the same MLST sequence type than between isolates belonging to different evolutionary lineages. Conclusion The variations in gene content observed among the investigated commensal E. faecalis is comparable to the genetic variation previously reported among strains of various origins thought to be representative of the major E. faecalis lineages. Previous MLST analysis of E. faecalis have identified so-called high-risk enterococcal clonal complexes (HiRECC), defined as genetically distinct subpopulations, epidemiologically associated with enterococcal infections. The observed correlation between CGH and MLST presented here, may offer a method for the identification of lineage-specific genes, and may therefore add clues on how to distinguish pathogenic from commensal E. faecalis. In this work, information on the core genome of E. faecalis is also substantially extended. PMID:19393078

Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.

PubMed

Riechmann, J L; Heard, J; Martin, G; Reuber, L; Jiang, C; Keddie, J; Adam, L; Pineda, O; Ratcliffe, O J; Samaha, R R; Creelman, R; Pilgrim, M; Broun, P; Zhang, J Z; Ghandehari, D; Sherman, B K; Yu, G

2000-12-15

The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms. Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants. Arabidopsis transcription factors that belong to families common to all eukaryotes do not share significant similarity with those of the other kingdoms beyond the conserved DNA binding domains, many of which have been arranged in combinations specific to each lineage. The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription.

THE M33 GLOBULAR CLUSTER SYSTEM WITH PAndAS DATA: THE LAST OUTER HALO CLUSTER?

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

Cockcroft, Robert; Harris, William E.; Ferguson, Annette M. N., E-mail: cockcroft@physics.mcmaster.ca, E-mail: harris@physics.mcmaster.ca, E-mail: ferguson@roe.ac.uk

2011-04-01

We use CFHT/MegaCam data to search for outer halo star clusters in M33 as part of the Pan-Andromeda Archaeological Survey. This work extends previous studies out to a projected radius of 50 kpc and covers over 40 deg{sup 2}. We find only one new unambiguous star cluster in addition to the five previously known in the M33 outer halo (10 kpc {<=} r {<=} 50 kpc). Although we identify 2440 cluster candidates of various degrees of confidence from our objective image search procedure, almost all of these are likely background contaminants, mostly faint unresolved galaxies. We measure the luminosity, color,more » and structural parameters of the new cluster in addition to the five previously known outer halo clusters. At a projected radius of 22 kpc, the new cluster is slightly smaller, fainter, and redder than all but one of the other outer halo clusters, and has g' {approx} 19.9, (g' - i') {approx} 0.6, concentration parameter c {approx} 1.0, a core radius r{sub c} {approx} 3.5 pc, and a half-light radius r{sub h} {approx} 5.5 pc. For M33 to have so few outer halo clusters compared to M31 suggests either tidal stripping of M33's outer halo clusters by M31, or a very different, much calmer accretion history of M33.« less

The M33 Globular Cluster System with PAndAS Data: the Last Outer Halo Cluster?

NASA Astrophysics Data System (ADS)

Cockcroft, Robert; Harris, William E.; Ferguson, Annette M. N.; Huxor, Avon; Ibata, Rodrigo; Irwin, Mike J.; McConnachie, Alan W.; Woodley, Kristin A.; Chapman, Scott C.; Lewis, Geraint F.; Puzia, Thomas H.

2011-04-01

We use CFHT/MegaCam data to search for outer halo star clusters in M33 as part of the Pan-Andromeda Archaeological Survey. This work extends previous studies out to a projected radius of 50 kpc and covers over 40 deg2. We find only one new unambiguous star cluster in addition to the five previously known in the M33 outer halo (10 kpc <= r <= 50 kpc). Although we identify 2440 cluster candidates of various degrees of confidence from our objective image search procedure, almost all of these are likely background contaminants, mostly faint unresolved galaxies. We measure the luminosity, color, and structural parameters of the new cluster in addition to the five previously known outer halo clusters. At a projected radius of 22 kpc, the new cluster is slightly smaller, fainter, and redder than all but one of the other outer halo clusters, and has g' ≈ 19.9, (g' - i') ≈ 0.6, concentration parameter c ≈ 1.0, a core radius rc ≈ 3.5 pc, and a half-light radius rh ≈ 5.5 pc. For M33 to have so few outer halo clusters compared to M31 suggests either tidal stripping of M33's outer halo clusters by M31, or a very different, much calmer accretion history of M33.

Understanding the direction of evolution in Burkholderia glumae through comparative genomics.

PubMed

Lee, Hyun-Hee; Park, Jungwook; Kim, Jinnyun; Park, Inmyoung; Seo, Young-Su

2016-02-01

Members of the genus Burkholderia occupy remarkably diverse niches, with genome sizes ranging from ~3.75 to 11.29 Mbp. The genome of Burkholderia glumae ranges in size from ~5.81 to 7.89 Mbp. Unlike other plant pathogenic bacteria, B. glumae can infect a wide range of monocot and dicot plants. Comparative genome analysis of B. glumae strains can provide insight into genome variation as well as differential features of whole metabolism or pathways between multiple strains of B. glumae infecting the same host. Comparative analysis of complete genomes among B. glumae BGR1, B. glumae LMG 2196, and B. glumae PG1 revealed the largest departmentalization of genes onto separate replicons in B. glumae BGR1 and considerable downsizing of the genome in B. glumae LMG 2196. In addition, the presence of large-scale evolutionary events such as rearrangement and inversion and the development of highly specialized systems were found to be related to virulence-associated features in the three B. glumae strains. This connection may explain why this bacterium broadens its host range and reinforces its interaction with hosts.

A New Determination of the Luminosity Function of the Galactic Halo.

NASA Astrophysics Data System (ADS)

Dawson, Peter Charles

The luminosity function of the galactic halo is determined by subtracting from the observed numbers of proper motion stars in the LHS Catalogue the expected numbers of main-sequence, degenerate, and giant stars of the disk population. Selection effects are accounted for by Monte Carlo simulations based upon realistic colour-luminosity relations and kinematic models. The catalogue is shown to be highly complete, and a calibration of the magnitude estimates therein is presented. It is found that, locally, the ratio of disk to halo material is close to 950, and that the mass density in main sequence and subgiant halo stars with 3 < M(,v) < 14 is about 2 x 10('-5) M(,o) pc('-3). With due allowance for white dwarfs and binaries, and taking into account the possibility of a moderate rate of halo rotation, it is argued that the total density does not much exceed 5 x 10('-5) M(,o) pc('-3), in which case the total mass interior to the sun is of the order of 5 x 10('8) M(,o) for a density distribution which projects to a de Vaucouleurs r(' 1/4) law. It is demonstrated that if the Wielen luminosity function is a faithful representation of the stellar distribution in the solar neighbourhood, then the observed numbers of large proper motion stars are inconsistent with the presence of an intermediate popula- tion at the level, and with the kinematics advocated recently by Gilmore and Reid. The initial mass function (IMF) of the halo is considered, and weak evidence is presented that its slope is at least not shallower than that of the disk population IMF. A crude estimate of the halo's age, based on a comparison of the main sequence turnoff in the reduced proper motion diagram with theoretical models is obtained; a tentative lower limit is 15 Gyr with a best estimate of between 15 and 18 Gyr. Finally, the luminosity function obtained here is compared with those determined in other investigations.

The Circumgalactic Medium in Massive Halos

NASA Astrophysics Data System (ADS)

Chen, Hsiao-Wen

This chapter presents a review of the current state of knowledge on the cool (T ˜ 104 K) halo gas content around massive galaxies at z ≈ 0. 2-2. Over the last decade, significant progress has been made in characterizing the cool circumgalactic gas in massive halos of M h ≈ 1012-14 M⊙ at intermediate redshifts using absorption spectroscopy. Systematic studies of halo gas around massive galaxies beyond the nearby universe are made possible by large spectroscopic samples of galaxies and quasars in public archives. In addition to accurate and precise constraints for the incidence of cool gas in massive halos, detailed characterizations of gas kinematics and chemical compositions around massive quiescent galaxies at z ≈ 0. 5 have also been obtained. Combining all available measurements shows that infalling clouds from external sources are likely the primary source of cool gas detected at halos and quasar bolometric luminosity remains a puzzle. Combining absorption-line studies with spatially resolved emission measurements of both gas and galaxies is the necessary next step to address remaining questions.

Impact of Neutrinos on Dark Matter Halo Environment

NASA Astrophysics Data System (ADS)

Court, Travis; Villaescusa-Navarro, Francisco

2018-01-01

The spatial clustering of galaxies is commonly used to infer the shape of the matter power spectrum and therefore to place constraints on the value of the cosmological parameters. In order to extract the maximum information from galaxy surveys it is required to provide accurate theoretical predictions. The first step to model galaxy clustering is to understand the spatial distribution of the structures where they reside: dark matter halos. I will show that the clustering of halos does not depend only on mass, but on other quantities like local matter overdensity. I will point out that halo clustering is also sensitive to the local overdensity of the cosmic neutrino background. I will show that splitting halos according to neutrino overdensity induces a very large scale-dependence bias, an effect that may lead to a new technique to constraint the sum of the neutrino masses.

Summary of the 2014 Beam-Halo Monitoring Workshop

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

Fisher, Alan

2015-09-25

Understanding and controlling beam halo is important for high-intensity hadron accelerators, for high-brightness electron linacs, and for low-emittance light sources. This can only be achieved by developing suitable diagnostics. The main challenge faced by such instrumentation is the high dynamic range needed to observe the halo in the presence of an intense core. In addition, measurements must often be made non-invasively. This talk summarizes the one-day workshop on Beam-Halo Monitoring that was held at SLAC on September 19 last year, immediately following IBIC 2014 in Monterey. Workshop presentations described invasive techniques using wires, screens, or crystal collimators, and non-invasive measurementsmore » with gas or scattered electrons. Talks on optical methods showed the close links between observing halo and astronomical problems like observing the solar corona or directly observing a planet orbiting another star.« less

Comparative genomics of transcriptional regulation of methionine metabolism in proteobacteria

DOE PAGES

Leyn, Semen A.; Suvorova, Inna A.; Kholina, Tatiana D.; ...

2014-11-20

Methionine metabolism and uptake genes in Proteobacteria are controlled by a variety of RNA and DNA regulatory systems. We have applied comparative genomics to reconstruct regulons for three known transcription factors, MetJ, MetR, and SahR, and three known riboswitch motifs, SAH, SAM-SAH, and SAM_alpha, in ~200 genomes from 22 taxonomic groups of Proteobacteria. We also identified two novel regulons: a SahR-like transcription factor SamR controlling various methionine biosynthesis genes in the Xanthomonadales group, and a potential RNA regulatory element with terminator-antiterminator mechanism controlling the metX or metZ genes in beta-proteobacteria. For each analyzed regulator we identified the core, taxon-specific andmore » genome-specific regulon members. By analyzing the distribution of these regulators in bacterial genomes and by comparing their regulon contents we elucidated possible evolutionary scenarios for the regulation of the methionine metabolism genes in Proteobacteria.« less

Search for and analysis of radioactive halos in lunar material

NASA Technical Reports Server (NTRS)

Gentry, R. V.

1976-01-01

The lunar halo search was conducted because halos in terrestrial minerals serve as pointers to localized radioactivity, and make possible analytical studies on the problems of isotopic dating and mode of crystallization of the host mineral. Ancillary studies were conducted on terrestrial halos and on certain samples of special origin such as tektites and meteorites.

Comparative Analysis of the First Complete Enterococcus faecium Genome

PubMed Central

Lam, Margaret M. C.; Seemann, Torsten; Bulach, Dieter M.; Gladman, Simon L.; Chen, Honglei; Haring, Volker; Moore, Robert J.; Ballard, Susan; Grayson, M. Lindsay; Johnson, Paul D. R.; Howden, Benjamin P.

2012-01-01

Vancomycin-resistant enterococci (VRE) are one of the leading causes of nosocomial infections in health care facilities around the globe. In particular, infections caused by vancomycin-resistant Enterococcus faecium are becoming increasingly common. Comparative and functional genomic studies of E. faecium isolates have so far been limited owing to the lack of a fully assembled E. faecium genome sequence. Here we address this issue and report the complete 3.0-Mb genome sequence of the multilocus sequence type 17 vancomycin-resistant Enterococcus faecium strain Aus0004, isolated from the bloodstream of a patient in Melbourne, Australia, in 1998. The genome comprises a 2.9-Mb circular chromosome and three circular plasmids. The chromosome harbors putative E. faecium virulence factors such as enterococcal surface protein, hemolysin, and collagen-binding adhesin. Aus0004 has a very large accessory genome (38%) that includes three prophage and two genomic islands absent among 22 other E. faecium genomes. One of the prophage was present as inverted 50-kb repeats that appear to have facilitated a 683-kb chromosomal inversion across the replication terminus, resulting in a striking replichore imbalance. Other distinctive features include 76 insertion sequence elements and a single chromosomal copy of Tn1549 containing the vanB vancomycin resistance element. A complete E. faecium genome will be a useful resource to assist our understanding of this emerging nosocomial pathogen. PMID:22366422

Comparative genomic analysis of Mycobacterium tuberculosis clinical isolates.

PubMed

Liu, Fei; Hu, Yongfei; Wang, Qi; Li, Hong Min; Gao, George F; Liu, Cui Hua; Zhu, Baoli

2014-06-13

Due to excessive antibiotic use, drug-resistant Mycobacterium tuberculosis has become a serious public health threat and a major obstacle to disease control in many countries. To better understand the evolution of drug-resistant M. tuberculosis strains, we performed whole genome sequencing for 7 M. tuberculosis clinical isolates with different antibiotic resistance profiles and conducted comparative genomic analysis of gene variations among them. We observed that all 7 M. tuberculosis clinical isolates with different levels of drug resistance harbored similar numbers of SNPs, ranging from 1409-1464. The numbers of insertion/deletions (Indels) identified in the 7 isolates were also similar, ranging from 56 to 101. A total of 39 types of mutations were identified in drug resistance-associated loci, including 14 previously reported ones and 25 newly identified ones. Sixteen of the identified large Indels spanned PE-PPE-PGRS genes, which represents a major source of antigenic variability. Aside from SNPs and Indels, a CRISPR locus with varied spacers was observed in all 7 clinical isolates, suggesting that they might play an important role in plasticity of the M. tuberculosis genome. The nucleotide diversity (Л value) and selection intensity (dN/dS value) of the whole genome sequences of the 7 isolates were similar. The dN/dS values were less than 1 for all 7 isolates (range from 0.608885 to 0.637365), supporting the notion that M. tuberculosis genomes undergo purifying selection. The Л values and dN/dS values were comparable between drug-susceptible and drug-resistant strains. In this study, we show that clinical M. tuberculosis isolates exhibit distinct variations in terms of the distribution of SNP, Indels, CRISPR-cas locus, as well as the nucleotide diversity and selection intensity, but there are no generalizable differences between drug-susceptible and drug-resistant isolates on the genomic scale. Our study provides evidence strengthening the notion that

Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains.

PubMed

Bhattacharyya, Anamitra; Stilwagen, Stephanie; Ivanova, Natalia; D'Souza, Mark; Bernal, Axel; Lykidis, Athanasios; Kapatral, Vinayak; Anderson, Iain; Larsen, Niels; Los, Tamara; Reznik, Gary; Selkov, Eugene; Walunas, Theresa L; Feil, Helene; Feil, William S; Purcell, Alexander; Lassez, Jean-Louis; Hawkins, Trevor L; Haselkorn, Robert; Overbeek, Ross; Predki, Paul F; Kyrpides, Nikos C

2002-09-17

Xylella fastidiosa (Xf) causes wilt disease in plants and is responsible for major economic and crop losses globally. Owing to the public importance of this phytopathogen we embarked on a comparative analysis of the complete genome of Xf pv citrus and the partial genomes of two recently sequenced strains of this species: Xf pv almond and Xf pv oleander, which cause leaf scorch in almond and oleander plants, respectively. We report a reanalysis of the previously sequenced Xf 9a5c (CVC, citrus) strain and the two "gapped" Xf genomes revealing ORFs encoding critical functions in pathogenicity and conjugative transfer. Second, a detailed whole-genome functional comparison was based on the three sequenced Xf strains, identifying the unique genes present in each strain, in addition to those shared between strains. Third, an "in silico" cellular reconstruction of these organisms was made, based on a comparison of their core functional subsystems that led to a characterization of their conjugative transfer machinery, identification of potential differences in their adhesion mechanisms, and highlighting of the absence of a classical quorum-sensing mechanism. This study demonstrates the effectiveness of comparative analysis strategies in the interpretation of genomes that are closely related.

Solar Radiation Measurements Onboard the Research Aircraft HALO

NASA Astrophysics Data System (ADS)

Lohse, I.; Bohn, B.; Werner, F.; Ehrlich, A.; Wendisch, M.

2014-12-01

Airborne measurements of the separated upward and downward components of solar spectral actinic flux densities for the determination of photolysis frequencies and of upward nadir spectral radiance were performed with the HALO Solar Radiation (HALO-SR) instrument package onboard the High Altitude and Long Range Research Aircraft (HALO). The instrumentation of HALO-SR is characterized and first measurement data from the Next-generation Aircraft Remote-Sensing for Validation Studies (NARVAL) campaigns in 2013 and 2014 are presented. The measured data are analyzed in the context of the retrieved microphysical and optical properties of clouds which were observed underneath the aircraft. Detailed angular sensitivities of the two optical actinic flux receivers were determined in the laboratory. The effects of deviations from the ideal response are investigated using radiative transfer calculations of atmospheric radiance distributions under various atmospheric conditions and different ground albedos. Corresponding correction factors are derived. Example photolysis frequencies are presented, which were sampled in the free troposphere and lower stratosphere over the Atlantic Ocean during the 2013/14 HALO NARVAL campaigns. Dependencies of photolysis frequencies on cloud cover, flight altitude and wavelength range of the photolysis process are investigated. Calculated actinic flux densities in the presence of clouds benefit from the measured spectral radiances. Retrieved cloud optical thicknesses and effective droplet radii are used as model input for the radiative transfer calculations. By comparison with the concurrent measurements of actinic flux densities the retrieval approach is validated. Acknowledgements: Funding by the Deutsche Forschungsgemeinschaft within the priority program HALO (BO 1580/4-1, WE 1900/21-1) is gratefully acknowledged.

Halo histories versus galaxy properties at z = 0 II: large-scale galactic conformity

NASA Astrophysics Data System (ADS)

Tinker, Jeremy L.; Hahn, ChangHoon; Mao, Yao-Yuan; Wetzel, Andrew R.; Conroy, Charlie

2018-06-01

Using group catalogues from the Sloan Digital Sky Survey (SDSS) Data Release 7, we measure galactic conformity in the local universe. We measure the quenched fraction of neighbour galaxies around isolated primary galaxies, dividing the isolated sample into star-forming and quiescent objects. We restrict our measurements to scales >1 Mpc to probe the correlations between halo formation histories. Over the stellar mass range 109.7 ≤ M*/M⊙ ≤ 1010.9, we find minimal evidence for conformity. We further compare these data to predictions of the halo age-matching model, in which the oldest galaxies are associated with the oldest haloes. For models with strong correlations between halo and stellar age, the conformity is too large to be consistent with the data. Weaker implementations of the age-matching model would not produce a detectable signal in SDSS data. We reproduce the results of Kauffmann et al., in which the star formation rates of neighbour galaxies are reduced around primary galaxies when the primaries are low star formers. However, we find this result is mainly driven by contamination in the isolation criterion; when removing the small fraction of satellite galaxies in the sample, the conformity signal largely goes away. Lastly, we show that small conformity signals, i.e. 2-5 per cent differences in the quenched fractions of neighbour galaxies, can be produced by mechanisms other than halo assembly bias. For example, if passive galaxies occupy more massive haloes than star-forming galaxies of the same stellar mass, a conformity signal that is consistent with recent measurements from PRIMUS (Berti et al.) can be produced.

Shrinking galaxy disks with fountain-driven accretion from the halo

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

Elmegreen, Bruce G.; Struck, Curtis; Hunter, Deidre A., E-mail: bge@watson.ibm.com, E-mail: curt@iastate.edu, E-mail: dah@lowell.edu

2014-12-01

Star formation in most galaxies requires cosmic gas accretion because the gas consumption time is short compared to the Hubble time. This accretion presumably comes from a combination of infalling satellite debris, cold flows, and condensation of hot halo gas at the cool disk interface, perhaps aided by a galactic fountain. In general, the accretion will have a different specific angular momentum than the part of the disk that receives it, even if the gas comes from the nearby halo. The gas disk then expands or shrinks over time. Here we show that condensation of halo gas at a ratemore » proportional to the star formation rate in the fountain model will preserve an initial shape, such as an exponential, with a shrinking scale length, leaving behind a stellar disk with a slightly steeper profile of younger stars near the center. This process is slow for most galaxies, producing imperceptible radial speeds, and it may be dominated by other torques, but it could be important for blue compact dwarfs, which tend to have large, irregular gas reservoirs and steep blue profiles in their inner stellar disks.« less

Effective Dark Matter Halo Catalog in f(R) Gravity.

PubMed

He, Jian-Hua; Hawken, Adam J; Li, Baojiu; Guzzo, Luigi

2015-08-14

We introduce the idea of an effective dark matter halo catalog in f(R) gravity, which is built using the effective density field. Using a suite of high resolution N-body simulations, we find that the dynamical properties of halos, such as the distribution of density, velocity dispersion, specific angular momentum and spin, in the effective catalog of f(R) gravity closely mimic those in the cold dark matter model with a cosmological constant (ΛCDM). Thus, when using effective halos, an f(R) model can be viewed as a ΛCDM model. This effective catalog therefore provides a convenient way for studying the baryonic physics, the galaxy halo occupation distribution and even semianalytical galaxy formation in f(R) cosmologies.

Bose-Einstein condensate haloes embedded in dark energy

NASA Astrophysics Data System (ADS)

Membrado, M.; Pacheco, A. F.

2018-04-01

Context. We have studied clusters of self-gravitating collisionless Newtonian bosons in their ground state and in the presence of the cosmological constant to model dark haloes of dwarf spheroidal (dSph) galaxies. Aim. We aim to analyse the influence of the cosmological constant on the structure of these systems. Observational data of Milky Way dSph galaxies allow us to estimate the boson mass. Methods: We obtained the energy of the ground state of the cluster in the Hartree approximation by solving a variational problem in the particle density. We have also developed and applied the virial theorem. Dark halo models were tested in a sample of 19 galaxies. Galaxy radii, 3D deprojected half-light radii, mass enclosed within them, and luminosity-weighted averages of the square of line-of-sight velocity dispersions are used to estimate the particle mass. Results: Cosmological constant repulsive effects are embedded in one parameter ξ. They are appreciable for ξ > 10-5. Bound structures appear for ξ ≤ ξc = 1.65 × 10-4, what imposes a lower bound for cluster masses as a function of the particle mass. In principle, these systems present tunnelling through a potential barrier; however, after estimating their mean lifes, we realize that their existence is not affected by the age of the Universe. When Milky Way dSph galaxies are used to test the model, we obtain 3.5-1.0+1.3 × 10-22 eV for the particle mass and a lower limit of 5.1-2.8+2.2 × 106 M⊙ for bound haloes. Conclusions: Our estimation for the boson mass is in agreement with other recent results which use different methods. From our particle mass estimation, the treated dSph galaxies would present dark halo masses 5-11 ×107 M⊙. With these values, they would not be affected by the cosmological constant (ξ < 10-8). However, dark halo masses smaller than 107 M⊙ (ξ > 10-5) would already feel their effects. Our model that includes dark energy allows us to deal with these dark haloes. Assuming quantities

Early predictive value of supine and upright X-ray films of odontoid fractures treated with halo-vest immobilization.

PubMed

Kim, David H; Vaccaro, Alexander R; Affonso, Jesse; Jenis, Louis; Hilibrand, Alan S; Albert, Todd J

2008-01-01

Although halo-vest immobilization remains a common form of treatment for type II odontoid fractures, nonunion and C1-2 instability may be the result in up to 20% to 40% of patients. Supine and upright lateral X-ray films may allow early identification of patients likely to fail halo-vest treatment and earlier surgical treatment with decreased morbidity from prolonged unsuccessful halo-vest immobilization. A prospective cohort study was performed. Twenty patients with type II odontoid fractures. Posttreatment nonunion and C1-2 instability as determined by plain X-ray films and computed tomography scan. Both supine and upright lateral X-ray films were obtained immediately after halo-vest application and at the 2-week, 6-week, and 3-month follow-up. Flexion-extension lateral X-ray films were obtained after halo-vest removal. Patients with nonunion or instability underwent computed tomography scan. Upright X-ray films were compared serially to identify loss of reduction. Pairs of supine and upright X-ray films were compared to measure any change in displacement or angulation upon transition from supine to upright position. Nonunion patients were compared with healed patients to determine any difference in fracture behavior based on serial supine and upright X-ray films. Twenty patients with type II odontoid fractures were identified during the study period. Three patients with multiple trauma underwent immediate surgical stabilization. Three elderly patients with nondisplaced fractures were treated in a cervical orthosis. Fourteen patients initiated and completed 3 months of halo-vest immobilization. After halo-vest removal, 4 of 14 patients (29%) showed radiographic nonunion or instability. In all 4 nonunion patients, supine and upright radiographs at 2 weeks revealed change in fracture angulation > or =5 degrees between the supine and upright positions. In three of these patients standard serial upright lateral X-ray films failed to identify any loss of reduction. In