Showing papers by "University of Georgia published in 2014"
TL;DR: The biodiversity of eukaryote species and their extinction rates, distributions, and protection is reviewed, and what the future rates of species extinction will be, how well protected areas will slow extinction Rates, and how the remaining gaps in knowledge might be filled are reviewed.
Abstract: Background A principal function of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) is to “perform regular and timely assessments of knowledge on biodiversity.” In December 2013, its second plenary session approved a program to begin a global assessment in 2015. The Convention on Biological Diversity (CBD) and five other biodiversity-related conventions have adopted IPBES as their science-policy interface, so these assessments will be important in evaluating progress toward the CBD’s Aichi Targets of the Strategic Plan for Biodiversity 2011–2020. As a contribution toward such assessment, we review the biodiversity of eukaryote species and their extinction rates, distributions, and protection. We document what we know, how it likely differs from what we do not, and how these differences affect biodiversity statistics. Interestingly, several targets explicitly mention “known species”—a strong, if implicit, statement of incomplete knowledge. We start by asking how many species are known and how many remain undescribed. We then consider by how much human actions inflate extinction rates. Much depends on where species are, because different biomes contain different numbers of species of different susceptibilities. Biomes also suffer different levels of damage and have unequal levels of protection. How extinction rates will change depends on how and where threats expand and whether greater protection counters them. Different visualizations of species biodiversity. ( A ) The distributions of 9927 bird species. ( B ) The 4964 species with smaller than the median geographical range size. ( C ) The 1308 species assessed as threatened with a high risk of extinction by BirdLife International for the Red List of Threatened Species of the International Union for Conservation of Nature. ( D ) The 1080 threatened species with less than the median range size. (D) provides a strong geographical focus on where local conservation actions can have the greatest global impact. Additional biodiversity maps are available at www.biodiversitymapping.org. Advances Recent studies have clarified where the most vulnerable species live, where and how humanity changes the planet, and how this drives extinctions. These data are increasingly accessible, bringing greater transparency to science and governance. Taxonomic catalogs of plants, terrestrial vertebrates, freshwater fish, and some marine taxa are sufficient to assess their status and the limitations of our knowledge. Most species are undescribed, however. The species we know best have large geographical ranges and are often common within them. Most known species have small ranges, however, and such species are typically newer discoveries. The numbers of known species with very small ranges are increasing quickly, even in well-known taxa. They are geographically concentrated and are disproportionately likely to be threatened or already extinct. We expect unknown species to share these characteristics. Current rates of extinction are about 1000 times the background rate of extinction. These are higher than previously estimated and likely still underestimated. Future rates will depend on many factors and are poised to increase. Finally, although there has been rapid progress in developing protected areas, such efforts are not ecologically representative, nor do they optimally protect biodiversity. Outlook Progress on assessing biodiversity will emerge from continued expansion of the many recently created online databases, combining them with new global data sources on changing land and ocean use and with increasingly crowdsourced data on species’ distributions. Examples of practical conservation that follow from using combined data in Colombia and Brazil can be found at www.savingspecies.org and www.youtube.com/watch?v=R3zjeJW2NVk.
2,360 citations
TL;DR: This article proposes rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggests a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and Archaea.
Abstract: Publicly available sequence databases of the small subunit ribosomal RNA gene, also known as 16S rRNA in bacteria and archaea, are growing rapidly, and the number of entries currently exceeds 4 million. However, a unified classification and nomenclature framework for all bacteria and archaea does not yet exist. In this Analysis article, we propose rational taxonomic boundaries for high taxa of bacteria and archaea on the basis of 16S rRNA gene sequence identities and suggest a rationale for the circumscription of uncultured taxa that is compatible with the taxonomy of cultured bacteria and archaea. Our analyses show that only nearly complete 16S rRNA sequences give accurate measures of taxonomic diversity. In addition, our analyses suggest that most of the 16S rRNA sequences of the high taxa will be discovered in environmental surveys by the end of the current decade.
1,755 citations
Duke University1, University of Texas at Austin2, Heidelberg Institute for Theoretical Studies3, American Museum of Natural History4, Beijing Genomics Institute5, Xi'an Jiaotong University6, New Mexico State University7, University of Sydney8, University of California9, Uppsala University10, University of Copenhagen11, Okinawa Institute of Science and Technology12, University of Georgia13, Griffith University14, Catalan Institution for Research and Advanced Studies15, Oak Ridge National Laboratory16, Joint Institute for Nuclear Research17, Aarhus University18, Washington University in St. Louis19, University of California, Santa Cruz20, Cardiff University21, Kunming Institute of Zoology22, China Agricultural University23, Louisiana State University24, Tulane University25, Copenhagen Zoo26, Oregon Health & Science University27, Federal University of Pará28, Technical University of Denmark29, Canterbury Museum30, Curtin University31, Novosibirsk State University32, Smithsonian Institution33, National University of Singapore34, National Museum of Natural History35, Nova Southeastern University36, Occidental College37, University of Edinburgh38, Harvard University39, University of California, San Francisco40, University of Florida41, University of Illinois at Urbana–Champaign42
TL;DR: A genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves recovered a highly resolved tree that confirms previously controversial sister or close relationships and identifies the first divergence in Neoaves, two groups the authors named Passerea and Columbea.
Abstract: To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
1,624 citations
Northwestern University1, University of Texas at Austin2, University of Alberta3, University of Arizona4, University of Georgia5, University of Florida6, Eastern Kentucky University7, American Museum of Natural History8, Pennsylvania State University9, Harvard University10, University of Cologne11, University of British Columbia12, Duke University13, Spanish National Research Council14, New York Botanical Garden15, Ludwig Maximilian University of Munich16, Université de Montréal17, Centre national de la recherche scientifique18, Chinese Academy of Sciences19, University of Michigan20, Donald Danforth Plant Science Center21
TL;DR: Strong and robust support is found for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
Abstract: Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
1,026 citations
United States Department of Energy1, North Dakota State University2, United States Department of Agriculture3, University of Georgia4, Institut national de la recherche agronomique5, Tennessee State University6, Colorado State University7, University of California, Davis8, Michigan State University9, University of Arizona10, University of Paris-Sud11, University of Nebraska–Lincoln12
TL;DR: 2 independent domestications from genetic pools that diverged before human colonization are confirmed and a set of genes linked with increased leaf and seed size are identified and combined with quantitative trait locus data from Mesoamerican cultivars.
Abstract: Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.
1,012 citations
University of British Columbia1, Canadian Institute for Advanced Research2, Monterey Bay Aquarium Research Institute3, Stony Brook University4, University of California, San Diego5, Brown University6, Marine Biological Laboratory7, University of Washington8, Dalhousie University9, National Center for Genome Resources10, Alfred Wegener Institute for Polar and Marine Research11, Rutgers University12, Texas A&M University13, University of Southern California14, University of Delaware15, Victoria University of Wellington16, University of Paris-Sud17, Columbia University18, University of Oslo19, University of Hawaii at Manoa20, University of Prince Edward Island21, University of Rhode Island22, Woods Hole Oceanographic Institution23, Jacobs University Bremen24, Max Planck Society25, Smith College26, University of South Alabama27, Saint Petersburg State University28, University of Geneva29, University of Connecticut30, Laval University31, University of Guelph32, University of North Carolina at Chapel Hill33, University of New Brunswick34, University of Camerino35, University of East Anglia36, Stazione Zoologica Anton Dohrn37, University of Georgia38, University of Technology, Sydney39, University of Puerto Rico40, University of Pisa41, Centre national de la recherche scientifique42, Colorado School of Mines43, Lund University44, University of Western Ontario45, California State University46, University of Texas at Austin47, Los Alamos National Laboratory48, Pierre-and-Marie-Curie University49, University of Oklahoma50, Plymouth Marine Laboratory51, Bigelow Laboratory For Ocean Sciences52, Princeton University53
TL;DR: In this paper, the authors describe a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans and their biology, evolution, and ecology.
Abstract: Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.
852 citations
Stanford University1, Lawrence Livermore National Laboratory2, University of California, Berkeley3, University of Toronto4, National Research Council5, Space Telescope Science Institute6, University of Arizona7, Princeton University8, University of California, Los Angeles9, Arizona State University10, University of California, Santa Cruz11, Université de Montréal12, Search for extraterrestrial intelligence13, Ames Research Center14, American Museum of Natural History15, Cornell University16, University of Georgia17, California Institute of Technology18, Johns Hopkins University19
TL;DR: Observations ofBeta Pictoris clearly detect the planet, Beta Pictoris b, in a single 60-s exposure with minimal postprocessing, and fitting the Keplerian orbit of Beta Pic b using the new position together with previous astrometry gives a factor of 3 improvement in most parameters over previous solutions.
Abstract: The Gemini Planet Imager is a dedicated facility for directly imaging and spectroscopically characterizing extrasolar planets. It combines a very high-order adaptive optics system, a diffraction-suppressing coronagraph, and an integral field spectrograph with low spectral resolution but high spatial resolution. Every aspect of the Gemini Planet Imager has been tuned for maximum sensitivity to faint planets near bright stars. During first-light observations, we achieved an estimated H band Strehl ratio of 0.89 and a 5-σ contrast of 10(6) at 0.75 arcseconds and 10(5) at 0.35 arcseconds. Observations of Beta Pictoris clearly detect the planet, Beta Pictoris b, in a single 60-s exposure with minimal postprocessing. Beta Pictoris b is observed at a separation of 434 ± 6 milliarcseconds (mas) and position angle 211.8 ± 0.5°. Fitting the Keplerian orbit of Beta Pic b using the new position together with previous astrometry gives a factor of 3 improvement in most parameters over previous solutions. The planet orbits at a semimajor axis of [Formula: see text] near the 3:2 resonance with the previously known 6-AU asteroidal belt and is aligned with the inner warped disk. The observations give a 4% probability of a transit of the planet in late 2017.
754 citations
TL;DR: A mixed methods study examined three instances of the flipped classroom across unique disciplines and developed a flipped classroom design framework and identified nine design principles.
Abstract: As a response to the call for technology enhanced, student-centered learning environments, the flipped classroom approach has drawn much attention from both the research and practice communities. Despite over fifteen years of flipped classroom implementation, design principles have been minimally elaborated upon in relation to diverse disciplinary contexts. Focusing on this gap, we engaged in a mixed methods study that examined three instances of the flipped classroom across unique disciplines and to extract specific design principles. Three instructors and 115 students enrolled in three separate classes in fall 2012 participated in the study. Building upon the Revised Community of Inquiry Framework, we developed a flipped classroom design framework and identified nine design principles.
716 citations
26 Mar 2014
TL;DR: Applied Research in Education and Behavioral Sciences, David L. Gast, Blair P. Lloyd, & Jennifer R. Ledford uncovers controversial and Critical Issues in Single Case Research.
Abstract: Chapter 1 Applied Research in Education and Behavioral Sciences, David L. Gast & Jennifer R. Ledford Chapter 2 Scientific Research in Educational and Clinical Settings, David L. Gast & James W. Tawney Chapter 3 Ethical Principles and Practices in Research, Linda Mechling, David L. Gast, & Justin Lane Chapter 4 Writing Tasks: Literature Reviews, Research Proposals, and Final Reports, Mark Wolery & Kathleen L. Lane Chapter 5 Scientific Research in Educational and Clinical Settings, David L. Gast & Jennifer R. Ledford Chapter 6 Replication, David L. Gast Chapter 7 Dependent Measures and Measurement Systems, Kevin Ayres & Jennifer R. Ledford Chapter 8 Visual Representation of Data, Amy D. Spriggs, Justin Lane, & David L. Gast Chapter 9 Visual Analysis of Graphic Data, David L. Gast & Amy D. Spriggs Chapter 10 Withdrawal and Reversal Designs, David L. Gast & Dianna H. Baekey Chapter 11 Multiple Baseline and Multiple Probe Designs, David L. Gast, Blair P. Lloyd, & Jennifer R. Ledford Chapter 12 Comparative and Other Designs, Mark Wolery, David L. Gast, & Jennifer R. Ledford Chapter 13 Combination and Other Designs, Jennifer R. Ledford & David L. Gast Chapter 14 Controversial and Critical Issues in Single Case Research, Jennifer R. Ledford, Mark Wolery, & David L. Gast
706 citations
14 Jan 2014
TL;DR: In this paper, the authors define educational design research as a genre of research in which the iterative development of solutions to practical and complex educational problems provides the setting for scientific inquiry.
Abstract: Educational design research is a genre of research in which the iterative development of solutions to practical and complex educational problems provides the setting for scientific inquiry. The solutions can be educational products, processes, programs, or policies. Educational design research not only targets solving significant problems facing educational practitioners but at the same time seeks to discover new knowledge that can inform the work of others facing similar problems. Working systematically and simultaneously toward these dual goals is perhaps the most defining feature of educational design research. This chapter seeks to clarify the nature of educational design research by distinguishing it from other types of inquiry conducted in the field of educational communications and technology. Examples of design research conducted by different researchers working in the field of educational communications and technology are described. The chapter concludes with a discussion of several important issues facing educational design researchers as they pursue future work using this innovative research approach.
692 citations
University of Georgia1, University of Colorado Boulder2, University of Wisconsin-Madison3, University of California, Los Angeles4, Yale University5, Indiana University of Pennsylvania6, University of Queensland7, Cornell University8, Purdue University9, Indiana University – Purdue University Indianapolis10
TL;DR: A summary of a meeting on assessment of course-based undergraduate research experiences (CUREs) is presented, including an operational definition of a CURE, a summary of research on CUREs, relevant findings from studies of undergraduate research internships, and recommendations for future research on and evaluation of CURESs.
Abstract: The Course-Based Undergraduate Research Experiences Network (CUREnet) was initiated in 2012 with funding from the National Science Foundation program for Research Coordination Networks in Undergraduate Biology Education. CUREnet aims to address topics, problems, and opportunities inherent to integrating research experiences into undergraduate courses. During CUREnet meetings and discussions, it became apparent that there is need for a clear definition of what constitutes a CURE and systematic exploration of what makes CUREs meaningful in terms of student learning. Thus, we assembled a small working group of people with expertise in CURE instruction and assessment to: 1) draft an operational definition of a CURE, with the aim of defining what makes a laboratory course or project a “research experience”; 2) summarize research on CUREs, as well as findings from studies of undergraduate research internships that would be useful for thinking about how students are influenced by participating in CUREs; and 3) identify areas of greatest need with respect to CURE assessment, and directions for future research on and evaluation of CUREs. This report summarizes the outcomes and recommendations of this meeting.
Liverpool School of Tropical Medicine1, University of Liverpool2, Queen Mary University of London3, Harvard University4, University of Oxford5, University of Birmingham6, Columbia University7, Sri Ramachandra University8, University of California, San Francisco9, University of California, Berkeley10, Malawi-Liverpool-Wellcome Trust Clinical Research Programme11, Johns Hopkins University12, Oregon Health & Science University13, Fudan University14, Health Effects Institute15, University of Georgia16, University of Aberdeen17, Ohio State University18
TL;DR: Evidence for the association between household air pollution and respiratory infections, respiratory tract cancers, and chronic lung diseases is reviewed, as well as study design issues and potential effective interventions to prevent these disease burdens.
TL;DR: It is shown that microbial-specific indoles regulated intestinal barrier function through the xenobiotic sensor, pregnane X receptor (PXR), and a direct chemical communication between the intestinal symbionts and PXR regulates mucosal integrity through a pathway that involves luminal sensing and signaling by TLR4.
Western Kentucky University1, Cooperative Institute for Research in Environmental Sciences2, University of Nebraska–Lincoln3, Purdue University4, University of Queensland5, Pennsylvania State University6, Cooperative Institute for Research in the Atmosphere7, Agriculture and Agri-Food Canada8, John Deere9, Oak Ridge National Laboratory10, University of Alabama in Huntsville11, University of Delaware12, University of Georgia13, Chinese Academy of Sciences14, University of Colorado Boulder15, Texas A&M University16, Tuskegee University17
TL;DR: In this article, the authors provide an overview and synthesis of some of the most notable types of land cover changes and their impacts on climate, including agriculture, deforestation and afforestation, desertification, and urbanization.
Abstract: Land cover changes (LCCs) play an important role in the climate system. Research over recent decades highlights the impacts of these changes on atmospheric temperature, humidity, cloud cover, circulation, and precipitation. These impacts range from the local- and regional-scale to sub-continental and global-scale. It has been found that the impacts of regional-scale LCC in one area may also be manifested in other parts of the world as a climatic teleconnection. In light of these findings, this article provides an overview and synthesis of some of the most notable types of LCC and their impacts on climate. These LCC types include agriculture, deforestation and afforestation, desertification, and urbanization. In addition, this article provides a discussion on challenges to, and future research directions in, assessing the climatic impacts of LCC.
TL;DR: A superconducting qubit architecture that combines high-coherence qubits and tunable qubit-qubit coupling that can be tuned dynamically with nanosecond resolution is introduced, making this architecture a versatile platform with applications ranging from quantum logic gates to quantum simulation.
Abstract: We introduce a superconducting qubit architecture that combines high-coherence qubits and tunable qubit-qubit coupling. With the ability to set the coupling to zero, we demonstrate that this architecture is protected from the frequency crowding problems that arise from fixed coupling. More importantly, the coupling can be tuned dynamically with nanosecond resolution, making this architecture a versatile platform with applications ranging from quantum logic gates to quantum simulation. We illustrate the advantages of dynamical coupling by implementing a novel adiabatic controlled-z gate, with a speed approaching that of single-qubit gates. Integrating coherence and scalable control, the introduced qubit architecture provides a promising path towards large-scale quantum computation and simulation.
University of Arizona1, University of Washington2, Beijing Institute of Genomics3, University of Alberta4, Northwestern University5, University of Texas at Austin6, University of Georgia7, University of Florida8, Pennsylvania State University9, Université de Montréal10, Centre national de la recherche scientifique11, Eastern Kentucky University12, University of British Columbia13, Harvard University14, University of Cologne15, Duke University16, Spanish National Research Council17, New York Botanical Garden18, Ludwig Maximilian University of Munich19, Chinese Academy of Sciences20, Donald Danforth Plant Science Center21, University of Michigan22
TL;DR: How to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize the gene and species trees of the 1KP project.
Abstract: The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.
TL;DR: In this paper, the authors examined the impact of Twitter followers, electronic word-of-mouth valence, and celebrity type on consumer behavior in Twitter-based marketing communication, applying social capital theory, social identity theory, source credibility, and extant literature on eWoM.
Abstract: Two experiments examined the impact of Twitter followers, electronic word-of-mouth (eWoM) valence, and celebrity type (prosocial versus antisocial) on consumer behavior in Twitter-based marketing communication, applying social capital theory, social identity theory, source credibility, and extant literature on eWoM. Experiment 1 demonstrated the main effect of number of followers on source credibility, and the interaction effect between eWoM valence and number of followers on product involvement, buying intention, and intention to pass along eWoM. Experiment 2 revealed the interaction effect of celebrity type and number of followers on social identification with the celebrity as well as the mediating effect of social identification.
TL;DR: Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass.
Abstract: Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.
TL;DR: In this paper, the authors argue that a social science approach that claims to be interpretive supports a positivist, quasi-statistical analytic practice (coding data) that has, unfortunately, been proliferated and formalized in too many introductory textbooks and university research courses.
Abstract: In 1991, Patti Lather (1991) called data analysis “the ‘black hole’ of qualitative research” (p. 149), and, as co-editors of this special issue on qualitative data analysis after coding, we suspect it still is. In fact, we think analysis—”thinking with theory” (Jackson & Mazzei, 2012)—is so difficult to describe and explain to the non-positivist—and to teach to our students—that we have resorted to equating qualitative data analysis with coding data. In other words, we teach analysis as coding because it is teachable. The critiques’ qualitative methodology endured during the debates about “scientifically based research” in the first decade of the 21st century surely intensified its already confused epistemological and ontological commitments. The incommensurability in this methodology is that a social science approach that claims to be interpretive supports a positivist, quasi-statistical analytic practice—coding data—that has, unfortunately, been proliferated and formalized in too many introductory textbooks and university research courses. A question we might ask at the outset is whether one would code data if one had not been taught to do so. We should state here at the beginning that we are not referring to the kind of analysis MacLure (2008) described as follows:
TL;DR: It is reported that the intestinal microbe Bacteroides fragilis modifies the homeostasis of host invariant natural killer T (iNKT) cells by supplementing the host's endogenous lipid antigen milieu with unique inhibitory sphingolipids, and suggests that the distinctive inhibitory capacity of GSL-Bf717 and similar molecules may prove useful in the treatment of autoimmune and allergic disorders in which iNKT cell activation is destructive.
TL;DR: An overview of the current state of knowledge of the chicken gastrointestinal microbiome focusing on spatial and temporal variability, the presence and importance of human pathogens, the influence of the microbiota on the immune system, and the importance of the microbiome for poultry nutrition is provided.
Abstract: The domestic chicken is a common model organism for human biological research and of course also forms the basis of a global protein industry. Recent methodological advances have spurred the recognition of microbiomes as complex communities with important influences on the health and disease status of the host. In this minireview, we provide an overview of the current state of knowledge of the chicken gastrointestinal microbiome focusing on spatial and temporal variability, the presence and importance of human pathogens, the influence of the microbiota on the immune system, and the importance of the microbiome for poultry nutrition. Review and meta-analysis of public data showed cecal communities dominated by Firmicutes and Bacteroides at the phylum level, while at finer levels of taxonomic resolution, a phylogenetically diverse assemblage of microorganisms appears to have similar metabolic functions that provide important benefits to the host as inferred from metagenomic data. This observation of functional redundancy may have important implications for management of the microbiome. We foresee advances in strategies to improve gut health in commercial operations through management of the intestinal microbiota as an alternative to in-feed subtherapeutic antibiotics, improvements in pre- and probiotics, improved management of polymicrobial poultry diseases, and better control of human pathogens via colonization reduction or competitive exclusion strategies.
TL;DR: The overall goal of this review is to present a new understanding of substance use disorders as viewed by recent advances in behavioral economics.
Abstract: The field of behavioral economics has made important inroads into the understanding of substance use disorders through the concept of reinforcer pathology. Reinforcer pathology refers to the joint effects of (a) the persistently high valuation of a reinforcer, broadly defined to include tangible commodities and experiences, and/or (b) the excessive preference for the immediate acquisition or consumption of a commodity despite long-term negative outcomes. From this perspective, reinforcer pathology results from the recursive interactions of endogenous person-level variables and exogenous environment-level factors. The current review describes the basic principles of behavioral economics that are central to reinforcer pathology, the processes that engender reinforcer pathology, and the approaches and procedures that can repair reinforcement pathologies. The overall goal of this review is to present a new understanding of substance use disorders as viewed by recent advances in behavioral economics.
TL;DR: It is shown that spatial and temporal patterns of genetic differentiation in Neotropical birds are highly discordant across lineages and are not reconcilable with a model linking speciation solely to landscape change, and the strongest predictors of speciation are the amount of time a lineage has persisted in the landscape and the ability of birds to move through the landscape matrix.
Abstract: Since the recognition that allopatric speciation can be induced by large-scale reconfigurations of the landscape that isolate formerly continuous populations, such as the separation of continents by plate tectonics, the uplift of mountains or the formation of large rivers, landscape change has been viewed as a primary driver of biological diversification. This process is referred to in biogeography as vicariance. In the most species-rich region of the world, the Neotropics, the sundering of populations associated with the Andean uplift is ascribed this principal role in speciation. An alternative model posits that rather than being directly linked to landscape change, allopatric speciation is initiated to a greater extent by dispersal events, with the principal drivers of speciation being organism-specific abilities to persist and disperse in the landscape. Landscape change is not a necessity for speciation in this model. Here we show that spatial and temporal patterns of genetic differentiation in Neotropical birds are highly discordant across lineages and are not reconcilable with a model linking speciation solely to landscape change. Instead, the strongest predictors of speciation are the amount of time a lineage has persisted in the landscape and the ability of birds to move through the landscape matrix. These results, augmented by the observation that most species-level diversity originated after episodes of major Andean uplift in the Neogene period, suggest that dispersal and differentiation on a matrix previously shaped by large-scale landscape events was a major driver of avian speciation in lowland Neotropical rainforests.
University of California, Davis1, University of Maryland, College Park2, Johns Hopkins University3, Children's Hospital Oakland Research Institute4, Indiana University5, University of Utah6, University of Florida7, United States Forest Service8, University of Georgia9, North Carolina State University10, Washington State University11, Texas A&M University12
TL;DR: In this paper, the authors used a whole genome shotgun approach relying on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding.
Abstract: The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination. We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome. In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied.
TL;DR: A draft genome sequence of mungbean is constructed to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species.
Abstract: Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.
TL;DR: Tenascins mediate both inflammatory and fibrotic processes to enable effective tissue repair and play roles in pathogenesis of Ehlers-Danlos, heart disease, and regeneration and recovery of musculo-tendinous tissue.
Abstract: Collagens are the most abundant components of the extracellular matrix and many types of soft tissues. Elastin is another major component of certain soft tissues, such as arterial walls and ligaments. Many other molecules, though lower in quantity, function as essential components of the extracellular matrix in soft tissues. Some of these are reviewed in this chapter. Besides their basic structure, biochemistry and physiology, their roles in disorders of soft tissues are discussed only briefly as most chapters in this volume deal with relevant individual compounds. Fibronectin with its muldomain structure plays a role of “master organizer” in matrix assembly as it forms a bridge between cell surface receptors, e.g., integrins, and compounds such collagen, proteoglycans and other focal adhesion molecules. It also plays an essential role in the assembly of fibrillin-1 into a structured network. Laminins contribute to the structure of the extracellular matrix (ECM) and modulate cellular functions such as adhesion, differentiation, migration, stability of phenotype, and resistance towards apoptosis. Though the primary role of fibrinogen is in clot formation, after conversion to fibrin by thrombin, it also binds to a variety of compounds, particularly to various growth factors, and as such fibrinogen is a player in cardiovascular and extracellular matrix physiology. Elastin, an insoluble polymer of the monomeric soluble precursor tropoelastin, is the main component of elastic fibers in matrix tissue where it provides elastic recoil and resilience to a variety of connective tissues, e.g., aorta and ligaments. Elastic fibers regulate activity of TGFβs through their association with fibrillin microfibrils. Elastin also plays a role in cell adhesion, cell migration, and has the ability to participate in cell signaling. Mutations in the elastin gene lead to cutis laxa. Fibrillins represent the predominant core of the microfibrils in elastic as well as non-elastic extracellular matrixes, and interact closely with tropoelastin and integrins. Not only do microfibrils provide structural integrity of specific organ systems, but they also provide a scaffold for elastogenesis in elastic tissues. Fibrillin is important for the assembly of elastin into elastic fibers. Mutations in the fibrillin-1 gene are closely associated with Marfan syndrome. Fibulins are tightly connected with basement membranes, elastic fibers and other components of extracellular matrix and participate in formation of elastic fibers. Tenascins are ECM polymorphic glycoproteins found in many connective tissues in the body. Their expression is regulated by mechanical stress both during development and in adulthood. Tenascins mediate both inflammatory and fibrotic processes to enable effective tissue repair and play roles in pathogenesis of Ehlers-Danlos, heart disease, and regeneration and recovery of musculo-tendinous tissue. One of the roles of thrombospondin 1 is activation of TGFβ. Increased expression of thrombospondin and TGFβ activity was observed in fibrotic skin disorders such as keloids and scleroderma. Cartilage oligomeric matrix protein (COMP) or thrombospondin-5 is primarily present in the cartilage. High levels of COMP are present in fibrotic scars and systemic sclerosis of the skin, and in tendon, especially with physical activity, loading and post-injury. It plays a role in vascular wall remodeling and has been found in atherosclerotic plaques as well.
TL;DR: In this paper, the authors examined the information content of the risk factor section and found that firms facing greater risk disclose more risk factors, and that the type of risk the firm faces determines whether it devotes a greater portion of its disclosures towards describing that risk type.
Abstract: Beginning in 2005, the Securities and Exchange Commission (SEC) mandated firms to include a “risk factor” section in their Form 10-K to discuss “the most significant factors that make the company speculative or risky.” In this study, we examine the information content of this newly created section and offer two main results. First, we find that firms facing greater risk disclose more risk factors, and that the type of risk the firm faces determines whether it devotes a greater portion of its disclosures towards describing that risk type. That is, managers provide risk factor disclosures that meaningfully reflect the risks they face. Second, we find that the information conveyed by risk factor disclosures is reflected in systematic risk, idiosyncratic risk, information asymmetry, and firm value. Overall, our evidence supports the SEC’s decision to mandate risk factor disclosures, as the disclosures appear to be firm-specific and useful to investors.
TL;DR: It is suggested that three mosquito species spanning the breadth of the Culicidae depend on their gut microbiome for development, and pyrosequencing of 16S rRNA provides new insights about the acquisition and structure of bacterial communities in mosquitoes.
Abstract: Field studies indicate adult mosquitoes (Culicidae) host low diversity communities of bacteria that vary greatly among individuals and species. In contrast, it remains unclear how adult mosquitoes acquire their microbiome, what influences community structure, and whether the microbiome is important for survival. Here, we used pyrosequencing of 16S rRNA to characterize the bacterial communities of three mosquito species reared under identical conditions. Two of these species, Aedes aegypti and Anopheles gambiae, are anautogenous and must blood-feed to produce eggs, while one, Georgecraigius atropalpus, is autogenous and produces eggs without blood feeding. Each mosquito species contained a low diversity community comprised primarily of aerobic bacteria acquired from the aquatic habitat in which larvae developed. Our results suggested that the communities in Ae. aegypti and An. gambiae larvae share more similarities with one another than with G. atropalpus. Studies with Ae. aegypti also strongly suggested that adults transstadially acquired several members of the larval bacterial community, but only four genera of bacteria present in blood fed females were detected on eggs. Functional assays showed that axenic larvae of each species failed to develop beyond the first instar. Experiments with Ae. aegypti indicated several members of the microbial community and Escherichia coli successfully colonized axenic larvae and rescued development. Overall, our results provide new insights about the acquisition and structure of bacterial communities in mosquitoes. They also indicate that three mosquito species spanning the breadth of the Culicidae depend on their gut microbiome for development.
TL;DR: This work sequencing the genomes of 145 diploid mutation accumulation (MA) lines of the budding yeast Saccharomyces cerevisiae identified nearly 1,000 mutations, a larger number than in any prior eukaryotic MA experiment as far as the authors are aware, and for the first time, in MA data, rates of context-dependent single-nucleotide mutations are estimated.
Abstract: Mutation is the ultimate source of genetic variation. The most direct and unbiased method of studying spontaneous mutations is via mutation accumulation (MA) lines. Until recently, MA experiments were limited by the cost of sequencing and thus provided us with small numbers of mutational events and therefore imprecise estimates of rates and patterns of mutation. We used whole-genome sequencing to identify nearly 1,000 spontaneous mutation events accumulated over ∼311,000 generations in 145 diploid MA lines of the budding yeast Saccharomyces cerevisiae. MA experiments are usually assumed to have negligible levels of selection, but even mild selection will remove strongly deleterious events. We take advantage of such patterns of selection and show that mutation classes such as indels and aneuploidies (especially monosomies) are proportionately much more likely to contribute mutations of large effect. We also provide conservative estimates of indel, aneuploidy, environment-dependent dominant lethal, and recessive lethal mutation rates. To our knowledge, for the first time in yeast MA data, we identified a sufficiently large number of single-nucleotide mutations to measure context-dependent mutation rates and were able to (i) confirm strong AT bias of mutation in yeast driven by high rate of mutations from C/G to T/A and (ii) detect a higher rate of mutation at C/G nucleotides in two specific contexts consistent with cytosine methylation in S. cerevisiae.
California Institute of Technology1, Janssen Pharmaceutica2, INAF3, Spanish National Research Council4, University of Oxford5, Centre national de la recherche scientifique6, University of Massachusetts Amherst7, University of Georgia8, Universidade Federal de Minas Gerais9, Katholieke Universiteit Leuven10, California State University11, University of Michigan12, University of Vienna13, Harvard University14, Lowell Observatory15, University of Wisconsin-Madison16, Wesleyan University17, New Mexico State University18, Search for extraterrestrial intelligence19, University of St Andrews20, Tel Aviv University21, Boston University22, National Autonomous University of Mexico23, European Space Agency24
TL;DR: The Coordinated Synoptic Investigation of NGC 2264 (CSI 2264) as discussed by the authors was a 30-day multi-wavelength photometric monitoring campaign on more than 1000 young star members using 16 telescopes.
Abstract: We present the Coordinated Synoptic Investigation of NGC 2264, a continuous 30 day multi-wavelength photometric monitoring campaign on more than 1000 young cluster members using 16 telescopes. The unprecedented combination of multi-wavelength, high-precision, high-cadence, and long-duration data opens a new window into the time domain behavior of young stellar objects. Here we provide an overview of the observations, focusing on results from Spitzer and CoRoT. The highlight of this work is detailed analysis of 162 classical T Tauri stars for which we can probe optical and mid-infrared flux variations to 1% amplitudes and sub-hour timescales. We present a morphological variability census and then use metrics of periodicity, stochasticity, and symmetry to statistically separate the light curves into seven distinct classes, which we suggest represent different physical processes and geometric effects. We provide distributions of the characteristic timescales and amplitudes and assess the fractional representation within each class. The largest category (>20%) are optical "dippers" with discrete fading events lasting ~1-5 days. The degree of correlation between the optical and infrared light curves is positive but weak; notably, the independently assigned optical and infrared morphology classes tend to be different for the same object. Assessment of flux variation behavior with respect to (circum)stellar properties reveals correlations of variability parameters with Hα emission and with effective temperature. Overall, our results point to multiple origins of young star variability, including circumstellar obscuration events, hot spots on the star and/or disk, accretion bursts, and rapid structural changes in the inner disk.