Showing 491 - 500 of 5831 Items
Rapid mechanisms for generating genome diversity: Whole ploidy shifts, aneuploidy, and loss of heterozygosity
Date: 2014-01-01
Creator: Richard J. Bennett, Anja Forche, Judith Berman
Access: Open access
- Human fungal pathogens can exist in a variety of ploidy states, including euploid and aneuploid forms. Ploidy change has a major impact on phenotypic properties, including the regulation of interactions with the human host. In addition, the rapid emergence of drug-resistant isolates is often associated with the formation of specific supernumerary chromosomes. Pathogens such as Candida albicans and Cryptococcus neoformans appear particularly well adapted for propagation in multiple ploidy states with novel pathways driving ploidy variation. In both species, heterozygous cells also readily undergo loss of heterozygosity (LOH), leading to additional phenotypic changes such as altered drug resistance. Here, we examine the sexual and parasexual cycles that drive ploidy variation in human fungal pathogens and discuss ploidy and LOH events with respect to their far-reaching roles in fungal adaptation and pathogenesis.
Two modes of transvection at the eyes absent gene of Drosophila demonstrate plasticity in transcriptional regulatory interactions in cis and in trans
Date: 2019-01-01
Creator: Katherine Tian, Rachel E. Henderson, Reyna Parker, Alexia Brown, Justine E., Johnson, Jack R. Bateman
Access: Open access
- For many genes, proper gene expression requires coordinated and dynamic interactions between multiple regulatory elements, each of which can either promote or silence transcription. In Drosophila, the complexity of the regulatory landscape is further complicated by the tight physical pairing of homologous chromosomes, which can permit regulatory elements to interact in trans, a phenomenon known as transvection. To better understand how gene expression can be programmed through cis- and trans-regulatory interactions, we analyzed transvection effects for a collection of alleles of the eyes absent (eya) gene. We find that trans-activation of a promoter by the eya eye-specific enhancers is broadly supported in many allelic backgrounds, and that the availability of an enhancer to act in trans can be predicted based on the molecular lesion of an eya allele. Furthermore, by manipulating promoter availability in cis and in trans, we demonstrate that the eye-specific enhancers of eya show plasticity in their promoter preference between two different transcriptional start sites, which depends on promoter competition between the two potential targets. Finally, we show that certain alleles of eya demonstrate pairing-sensitive silencing resulting from trans-interactions between Polycomb Response Elements (PREs), and genetic and genomic data support a general role for PcG proteins in mediating transcriptional silencing at eya. Overall, our data highlight how eya gene regulation relies upon a complex but plastic interplay between multiple enhancers, promoters, and PREs.
Economic-based projections of future land use in the conterminous United States under alternative policy scenarios
Date: 2012-04-01
Creator: V. C. Radeloff, E. Nelson, A. J. Plantinga, D. J. Lewis, D., Helmers, J. J. Lawler, J. C. Withey, F. Beaudry, S. Martinuzzi
Access: Open access
- Land-use change significantly contributes to biodiversity loss, invasive species spread, changes in biogeochemical cycles, and the loss of ecosystem services. Planning for a sustainable future requires a thorough understanding of expected land use at the fine spatial scales relevant for modeling many ecological processes and at dimensions appropriate for regional or national-level policy making. Our goal was to construct and parameterize an econometric model of land-use change to project future land use to the year 2051 at a fine spatial scale across the conterminous United States under several alternative land-use policy scenarios. We parameterized the econometric model of land-use change with the National Resource Inventory (NRI) 1992 and 1997 land-use data for 844 000 sample points. Land-use transitions were estimated for five land-use classes (cropland, pasture, range, forest, and urban). We predicted land-use change under four scenarios: business-as-usual, afforestation, removal of agricultural subsidies, and increased urban rents. Our results for the business-as-usual scenario showed widespread changes in land use, affecting 36% of the land area of the conterminous United States, with large increases in urban land (79%) and forest (7%), and declines in cropland (\-16%) and pasture (\-13%). Areas with particularly high rates of land-use change included the larger Chicago area, parts of the Pacific Northwest, and the Central Valley of California. However, while land-use change was substantial, differences in results among the four scenarios were relatively minor. The only scenario that was markedly different was the afforestation scenario, which resulted in an increase of forest area that was twice as high as the business-as-usual scenario. Land-use policies can affect trends, but only so much. The basic economic and demographic factors shaping land-use changes in the United States are powerful, and even fairly dramatic policy changes, showed only moderate deviations from the business-as-usual scenario. Given the magnitude of predicted land-use change, any attempts to identify a sustainable future or to predict the effects of climate change will have to take likely land-use changes into account. Econometric models that can simulate land-use change for broad areas with fine resolution are necessary to predict trends in ecosystem service provision and biodiversity persistence. © 2012 by the Ecological Society of America.
Tempered, invariant, positive-definite distributions on SU(1, 1)/{± 1}
Date: 1984-01-01
Creator: William H. Barker
Access: Open access
The 'obligate diploid' Candida albicans forms mating-competent haploids
Date: 2013-02-07
Creator: Meleah A. Hickman, Guisheng Zeng, Anja Forche, Matthew P. Hirakawa, Darren, Abbey, Benjamin D. Harrison, Yan Ming Wang, Ching Hua Su, Richard J. Bennett, Yue Wang, Judith Berman
Access: Open access
- Candida albicans, the most prevalent human fungal pathogen, is considered to be an obligate diploid that carries recessive lethal mutations throughout the genome. Here we demonstrate that C. albicans has a viable haploid state that can be derived from diploid cells under in vitro and in vivo conditions, and that seems to arise through a concerted chromosome loss mechanism. Haploids undergo morphogenetic changes like those of diploids, including the yeast-hyphal transition, chlamydospore formation and a white-opaque switch that facilitates mating. Haploid opaque cells of opposite mating type mate efficiently to regenerate the diploid form, restoring heterozygosity and fitness. Homozygous diploids arise spontaneously by auto-diploidization, and both haploids and auto-diploids show a similar reduction in fitness, in vitro and in vivo, relative to heterozygous diploids, indicating that homozygous cell types are transient in mixed populations. Finally, we constructed stable haploid strains with multiple auxotrophies that will facilitate molecular and genetic analyses of this important pathogen. © 2013 Macmillan Publishers Limited. All rights reserved.
BCJ relations from a new symmetry of gauge-theory amplitudes
Date: 2016-10-01
Creator: Robert W. Brown, Stephen G. Naculich
Access: Open access
- We introduce a new set of symmetries obeyed by tree-level gauge-theory amplitudes involving at least one gluon. The symmetry acts as a momentum-dependent shift on the color factors of the amplitude. Using the radiation vertex expansion, we prove the invariance under this color-factor shift of the n-gluon amplitude, as well as amplitudes involving massless or massive particles in an arbitrary representation of the gauge group with spin zero, one-half, or one. The Bern-Carrasco-Johansson relations are a direct consequence of this symmetry. We also introduce the cubic vertex expansion of an amplitude, and use it to derive a generalized-gauge-invariant constraint on the kinematic numerators of the amplitude. We show that the amplitudes of the bi-adjoint scalar theory are invariant under the color-factor symmetry, and use this to derive the null eigenvectors of the propagator matrix. We generalize the color-factor shift to loop level, and prove the invariance under this shift of one-loop n-gluon amplitudes in any theory that admits a color-kinematic-dual representation of numerators. We show that the one-loop color-factor symmetry implies known relations among the integrands of one-loop color-ordered amplitudes.
Genome plasticity in candida albicans is driven by long repeat sequences
Date: 2019-06-01
Creator: Robert T. Todd, Tyler D. Wikoff, Anja Forche, Anna Selmecki
Access: Open access
- Genome rearrangements resulting in copy number variation (CNV) and loss of heterozygosity (LOH) are frequently observed during the somatic evolution of cancer and promote rapid adaptation of fungi to novel environments. In the human fungal pathogen Candida albicans, CNV and LOH confer increased virulence and antifungal drug resistance, yet the mechanisms driving these rearrangements are not completely understood. Here, we unveil an extensive array of long repeat sequences (65–6499 bp) that are associated with CNV, LOH, and chromosomal inversions. Many of these long repeat sequences are uncharacterized and encompass one or more coding sequences that are actively transcribed. Repeats associated with genome rearrangements are predominantly inverted and separated by up to ~1.6 Mb, an extraordinary distance for homology-based DNA repair/recombination in yeast. These repeat sequences are a significant source of genome plasticity across diverse strain backgrounds including clinical, environmental, and experimentally evolved isolates, and represent previously uncharacterized variation in the reference genome.
An overview of approaches and challenges for retrieving marine inherent optical properties from ocean color remote sensing
Date: 2018-01-01
Creator: P. Jeremy Werdell, Lachlan I.W. McKinna, Emmanuel Boss, Steven G. Ackleson, Susanne E., Craig, Watson W. Gregg, Zhongping Lee, Stéphane Maritorena, Collin S. Roesler, Cécile S. Rousseaux, Dariusz Stramski, James M. Sullivan, Michael S. Twardowski, Maria Tzortziou, Xiaodong Zhang
Access: Open access
- Ocean color measured from satellites provides daily global, synoptic views of spectral water-leaving reflectances that can be used to generate estimates of marine inherent optical properties (IOPs). These reflectances, namely the ratio of spectral upwelled radiances to spectral downwelled irradiances, describe the light exiting a water mass that defines its color. IOPs are the spectral absorption and scattering characteristics of ocean water and its dissolved and particulate constituents. Because of their dependence on the concentration and composition of marine constituents, IOPs can be used to describe the contents of the upper ocean mixed layer. This information is critical to further our scientific understanding of biogeochemical oceanic processes, such as organic carbon production and export, phytoplankton dynamics, and responses to climatic disturbances. Given their importance, the international ocean color community has invested significant effort in improving the quality of satellite-derived IOP products, both regionally and globally. Recognizing the current influx of data products into the community and the need to improve current algorithms in anticipation of new satellite instruments (e.g., the global, hyperspectral spectroradiometer of the NASA Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission), we present a synopsis of the current state of the art in the retrieval of these core optical properties. Contemporary approaches for obtaining IOPs from satellite ocean color are reviewed and, for clarity, separated based their inversion methodology or the type of IOPs sought. Summaries of known uncertainties associated with each approach are provided, as well as common performance metrics used to evaluate them. We discuss current knowledge gaps and make recommendations for future investment for upcoming missions whose instrument characteristics diverge sufficiently from heritage and existing sensors to warrant reassessing current approaches.
Stolen Future, Broken Present: The Human Significance of Climate Change
Date: 2014-01-01
Creator: David A Collings
Access: Open access
- This book argues that climate change has a devastating effect on how we think about the future. Once several positive feedback loops in Earth’s dynamic systems, such as the melting of the Arctic icecap or the drying of the Amazon, cross the point of no return, the biosphere is likely to undergo severe and irreversible warming. Nearly everything we do is premised on the assumption that the world we know will endure into the future and provide a sustaining context for our activities. But today the future of a viable biosphere, and thus the purpose of our present activities, is put into question. A disappearing future leads to a broken present, a strange incoherence in the feel of everyday life. We thus face the unprecedented challenge of salvaging a basis for our lives today. That basis, this book argues, may be found in our capacity to assume an infinite responsibility for ecological disaster and, like the biblical Job, to respond with awe to the alien voice that speaks from the whirlwind. By owning disaster and accepting our small place within the inhuman forces of the biosphere, we may discover how to live with responsibility and serenity whatever may come. (Publisher's Description) Freely available online at https://quod.lib.umich.edu/o/ohp/12832550.0001.001.
With age comes immaturity: Do countries with older populations issue shorter maturity debt?
Date: 2021-12-01
Creator: Gonca Senel, Mark L.J. Wright
Access: Open access
- Recent work has found that countries with older populations face steeper yield curves and issue shorter maturity debt than do younger countries. We reexamine these findings using a new database of public debt maturity and yields for OECD countries. We first show that the behavior of eurozone countries in the pre-euro period drives these results. Next, including more recent data from the post-euro period, we show that the relationship between population age, maturity, and yield curve slopes disappears. This finding is robust to excluding high-credit-risk countries. Last, we show that these patterns reemerge after the European debt crisis, suggesting that eurozone capital markets have resegmented.