Bioinformatic approaches for genome finishing

Husemann P, Tauch A. Bioinformatic approaches for genome finishing. Bielefeld: Universitätsbibliothek Bielefeld; 2011

The EDGE-CALIFA Survey: Interferometric Observations of 126 Galaxies with CARMA

We present interferometric CO observations, made with the Combined Array for Millimeter-wave Astronomy (CARMA) interferometer, of galaxies from the Extragalactic Database for Galaxy Evolution survey (EDGE). These galaxies are selected from the Calar Alto Legacy Integral Field Area (CALIFA) sample, mapped with optical integral field spectroscopy. EDGE provides good-quality CO data (3σ sensitivity before inclination correction, resolution ∼1.4 kpc) for 126 galaxies, constituting the largest interferometric CO survey of galaxies in the nearby universe. We describe the survey and data characteristics and products, then present initial science results. We find that the exponential scale lengths of the molecular, stellar, and star-forming disks are approximately equal, and galaxies that are more compact in molecular gas than in stars tend to show signs of interaction. We characterize the molecular-to-stellar ratio as a function of Hubble type and stellar mass and present preliminary results on the resolved relations between the molecular gas, stars, and star-formation rate. We then discuss the dependence of the resolved molecular depletion time on stellar surface density, nebular extinction, and gas metallicity. EDGE provides a key data set to address outstanding topics regarding gas and its role in star formation and galaxy evolution, which will be publicly available on completion of the quality assessment.Fil: Bolatto, Alberto. University of Maryland; Estados UnidosFil: Wong, Tony. University of Illinois at Urbana; Estados UnidosFil: Utomo, Dyas. University of California at Berkeley; Estados UnidosFil: Blitz, Leo. University of California at Berkeley; Estados UnidosFil: Vogel, Stuart N.. University of Maryland; Estados UnidosFil: Sánchez, Sebastián F.. Universidad Nacional Autónoma de México; MéxicoFil: Barrera-Ballesteros, Jorge. University Johns Hopkins; Estados UnidosFil: Cao, Yixian. University of Illinois; Estados UnidosFil: Colombo, Dario. Max Planck Institut Fur Radioastronomie; AlemaniaFil: Dannerbauer, Helmut. Universidad de La Laguna; EspañaFil: García-Benito, Rubén. Instituto de Astrofísica de Andalucía; EspañaFil: Herrera-Camus, Rodrigo. Max Planck Institute für Extraterrestrische Physik; AlemaniaFil: Husemann, Bernd. Max-Planck-Institut für Astronomie; AlemaniaFil: Kalinova, Veselina. Max Planck Institut für Radioastronomie; AlemaniaFil: Leroy, Adam K.. Ohio State University; Estados UnidosFil: Leung, Gigi. Max-Planck-Institut für Astronomie; AlemaniaFil: Levy, Rebecca C.. University of Maryland; Estados UnidosFil: Mast, Damian. Observatorio Astronomico de la Universidad Nacional de Cordoba; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba; ArgentinaFil: Ostriker, Eve. University of Princeton; Estados UnidosFil: Rosolowsky, Erik. University of Alberta; CanadáFil: Sandstrom, Karin M.. University of California at San Diego; Estados UnidosFil: Teuben, Peter. University of Maryland; Estados UnidosFil: Van De Ven, Glenn. Max-Planck-Institut für Astronomie; AlemaniaFil: Walter, Fabian. Max-Planck-Institut für Astronomie; Alemani

Rebuilding the hematopoietic stem cell niche: Recent developments and future prospects

Hematopoietic stem cells (HSCs) have proven their clinical relevance in stem cell transplantation to cure patients with hematological disorders. Key to their regenerative potential is their natural microenvironment – their niche – in the bone marrow (BM). Developments in the field of biomaterials enable the recreation of such environments with increasing preciseness in the laboratory. Such artificial niches help to gain a fundamental understanding of the biophysical and biochemical processes underlying the interaction of HSCs with the materials in their environment and the disturbance of this interplay during diseases affecting the BM. Artificial niches also have the potential to multiply HSCs in vitro, to enable the targeted differentiation of HSCs into mature blood cells or to serve as drug-testing platforms. In this review, we will introduce the importance of artificial niches followed by the biology and biophysics of the natural archetype. We will outline how 2D biomaterials can be used to dissect the complexity of the natural niche into individual parameters for fundamental research and how 3D systems evolved from them. We will present commonly used biomaterials for HSC research and their applications. Finally, we will highlight two areas in the field of HSC research, which just started to unlock the possibilities provided by novel biomaterials, in vitro blood production and studying the pathophysiology of the niche in vitro. With these contents, the review aims to give a broad overview of the different biomaterials applied for HSC research and to discuss their potentials, challenges and future directions in the field. Statement of significance Hematopoietic stem cells (HSCs) are multipotent cells responsible for maintaining the turnover of all blood cells. They are routinely applied to treat patients with hematological diseases. This high clinical relevance explains the necessity of multiplication or differentiation of HSCs in the laboratory, which is hampered by the missing natural microenvironment – the so called niche. Biomaterials offer the possibility to mimic the niche and thus overcome this hurdle. The review introduces the HSC niche in the bone marrow and discusses the utility of biomaterials in creating artificial niches. It outlines how 2D systems evolved into sophisticated 3D platforms, which opened the gateway to applications such as, expansion of clinically relevant HSCs, in vitro blood production, studying niche pathologies and drug testing

The EDGE-CALIFA survey: Using optical extinction to probe the spatially resolved distribution of gas in nearby galaxies

We present an empirical relation between the cold gas surface density (Σgas) and the optical extinction (AV) in a sample of 103 galaxies from the Extragalactic Database for Galaxy Evolution (EDGE) survey. This survey provides CARMA interferometric CO observations for 126 galaxies included in the Calar Alto Legacy Integral Field Area (CALIFA) survey. The matched, spatially resolved nature of these data sets allows us to derive the Σgas-AV relation on global, radial, and kpc (spaxel) scales. We determine AV from the Balmer decrement (H α/H β). We find that the best fit for this relation is Σgas (M☉ pc−2) ∼ 26 × AV (mag), and that it does not depend on the spatial scale used for the fit. However, the scatter in the fits increases as we probe smaller spatial scales, reflecting the complex relative spatial distributions of stars, gas, and dust. We investigate the Σgas/AV ratio on radial and spaxel scales as a function of EW(H α). We find that at larger values of EW(H α ) (i.e. actively star-forming regions) this ratio tends to converge to twice the value expected for a foreground dust screen geometry (∼30 M☉ pc−2 mag−1). On radial scales, we do not find a significant relation between the Σgas/AV ratio and the ionized gas metallicity. We contrast our estimates of Σgas using AV with compilations in the literature of the gas fraction on global and radial scales as well as with well-known scaling relations such as the radial star formation law and the Σgas-Σ∗ relation. These tests show that optical extinction is a reliable proxy for estimating Σgas in the absence of direct sub/millimeter observations of the cold gas.Fil: Barrera Ballesteros, Jorge K.. Universidad Nacional Autónoma de México; MéxicoFil: Utomo, Dyas. Ohio State University; Estados UnidosFil: Bolatto, Alberto. University of Maryland; Estados UnidosFil: Sánchez, Sebastián F.. Universidad Nacional Autónoma de México; MéxicoFil: Vogel, Stuart N.. University of Maryland; Estados UnidosFil: Wong, Tony. University of Illinois; Estados UnidosFil: Levy, Rebecca C.. University of Maryland; Estados UnidosFil: Colombo, Dario. Max Planck Institut Fur Radioastronomie; AlemaniaFil: Kalinova, Veselina. Max Planck Institut Fur Radioastronomie; AlemaniaFil: Teuben, Peter. University of Maryland; Estados UnidosFil: García Benito, Rubén. Instituto de Astrofísica de Andalucía; EspañaFil: Husemann, Bernd. Max Planck Institut Fur Astronomie; AlemaniaFil: Mast, Damian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Astronomía Teórica y Experimental. Universidad Nacional de Córdoba. Observatorio Astronómico de Córdoba. Instituto de Astronomía Teórica y Experimental; ArgentinaFil: Blitz, Leo. University of California at Berkeley; Estados Unido

The Mice at play in the CALIFA survey: A case study of a gas-rich major merger between first passage and coalescence

We present optical integral field spectroscopy (IFS) observations of the Mice, a major merger between two massive (>10^11Msol) gas-rich spirals NGC4676A and B, observed between first passage and final coalescence. The spectra provide stellar and gas kinematics, ionised gas properties and stellar population diagnostics, over the full optical extent of both galaxies. The Mice provide a perfect case study highlighting the importance of IFS data for improving our understanding of local galaxies. The impact of first passage on the kinematics of the stars and gas has been significant, with strong bars likely induced in both galaxies. The barred spiral NGC4676B exhibits a strong twist in both its stellar and ionised gas disk. On the other hand, the impact of the merger on the stellar populations has been minimal thus far: star formation induced by the recent close passage has not contributed significantly to the global star formation rate or stellar mass of the galaxies. Both galaxies show bicones of high ionisation gas extending along their minor axes. In NGC4676A the high gas velocity dispersion and Seyfert-like line ratios at large scaleheight indicate a powerful outflow. Fast shocks extend to ~6.6kpc above the disk plane. The measured ram pressure and mass outflow rate (~8-20Msol/yr) are similar to superwinds from local ULIRGs, although NGC4676A has only a moderate infrared luminosity of 3x10^10Lsol. Energy beyond that provided by the mechanical energy of the starburst appears to be required to drive the outflow. We compare the observations to mock kinematic and stellar population maps from a merger simulation. The models show little enhancement in star formation during and following first passage, in agreement with the observations. We highlight areas where IFS data could help further constrain the models.Comment: 23 pages, 13 figures, accepted to A&A. A version with a complete set of high resolution figures is available here: http://www-star.st-and.ac.uk/~vw8/resources/mice_v8_astroph.pd

Phylogenetic comparative assembly

Husemann P, Stoye J. Phylogenetic Comparative Assembly. Algorithms for Molecular Biology. 2010;5(1): 3.BACKGROUND:Recent high throughput sequencing technologies are capable of generating a huge amount of data for bacterial genome sequencing projects. Although current sequence assemblers successfully merge the overlapping reads, often several contigs remain which cannot be assembled any further. It is still costly and time consuming to close all the gaps in order to acquire the whole genomic sequence. RESULTS:Here we propose an algorithm that takes several related genomes and their phylogenetic relationships into account to create a graph that contains the likelihood for each pair of contigs to be adjacent. Subsequently, this graph can be used to compute a layout graph that shows the most promising contig adjacencies in order to aid biologists in finishing the complete genomic sequence. The layout graph shows unique contig orderings where possible, and the best alternatives where necessary. CONCLUSIONS:Our new algorithm for contig ordering uses sequence similarity as well as phylogenetic information to estimate adjacencies of contigs. An evaluation of our implementation shows that it performs better than recent approaches while being much faster at the same tim

Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set

We report a measurement of the bottom-strange meson mixing phase \beta_s using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays in which the quark-flavor content of the bottom-strange meson is identified at production. This measurement uses the full data set of proton-antiproton collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity. We report confidence regions in the two-dimensional space of \beta_s and the B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2, -1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in agreement with the standard model expectation. Assuming the standard model value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +- 0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +- 0.009 (syst) ps, which are consistent and competitive with determinations by other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012

Marketing as a means to transformative social conflict resolution: lessons from transitioning war economies and the Colombian coffee marketing system

Social conflicts are ubiquitous to the human condition and occur throughout markets, marketing processes, and marketing systems.When unchecked or unmitigated, social conflict can have devastating consequences for consumers, marketers, and societies, especially when conflict escalates to war. In this article, the authors offer a systemic analysis of the Colombian war economy, with its conflicted shadow and coping markets, to show how a growing network of fair-trade coffee actors has played a key role in transitioning the country’s war economy into a peace economy. They particularly draw attention to the sources of conflict in this market and highlight four transition mechanisms — i.e., empowerment, communication, community building and regulation — through which marketers can contribute to peacemaking and thus produce mutually beneficial outcomes for consumers and society. The article concludes with a discussion of implications for marketing theory, practice, and public policy

The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence

Trost E, Ott L, Schneider J, et al. The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence. BMC Genomics. 2010;11(1): 728

How genomics can help biodiversity conservation

The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.info:eu-repo/semantics/publishedVersio