Contextual organismality: Beyond pattern to process in the emergence of organisms

Biologists have taken the concept of organism largely for granted. However, advances in the study of chimerism, symbiosis, bacterial-eukaryote associations, and microbial behavior have prompted a redefinition of organisms as biological entities exhibiting low conflict and high cooperation among their parts. This expanded view identifies organisms in evolutionary time. However, the ecological processes, mechanisms, and traits that drive the formation of organisms remain poorly understood. Recognizing that organismality can be context dependent, we advocate elucidating the ecological contexts under which entities do or do not act as organisms. Here we develop a "contextual organismality" framework and provide examples of entities, such as honey bee colonies, tumors, and bacterial swarms, that can act as organisms under specific life history, resource, or other ecological circumstances. We suggest that context dependence may be a stepping stone to the development of increased organismal unification, as the most integrated biological entities generally show little context dependence. Recognizing that organismality is contextual can identify common patterns and testable hypotheses across different entities. The contextual organismality framework can illuminate timeless as well as pressing issues in biology, including topics as disparate as cancer emergence, genomic conflict, evolution of symbiosis, and the role of the microbiota in impacting host phenotype.John Templeton FoundationVersion of record online: 27 October 2016; published open access.This item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Black box of phage-bacterium interactions : exploring alternative phage infection strategies

The canonical lytic-lysogenic binary has been challenged in recent years, as more evidence has emerged on alternative bacteriophage infection strategies. These infection modes are little studied, and yet they appear to be more abundant and ubiquitous in nature than previously recognized, and can play a significant role in the ecology and evolution of their bacterial hosts. In this review, we discuss the extent, causes and consequences of alternative phage lifestyles, and clarify conceptual and terminological confusion to facilitate research progress. We propose distinct definitions for the terms 'pseudolysogeny' and 'productive or non-productive chronic infection', and distinguish them from the carrier state life cycle, which describes a population-level phenomenon. Our review also finds that phages may change their infection modes in response to environmental conditions or the physiological state of the host cell. We outline known molecular mechanisms underlying the alternative phage-host interactions, including specific genetic pathways and their considerable biotechnological potential. Moreover, we discuss potential implications of the alternative phage lifestyles for microbial biology and ecosystem functioning, as well as applied topics such as phage therapy.Peer reviewe

Radio continuum properties of luminous infrared galaxies. Identifying the presence of an AGN in the radio

Luminous infrared galaxies are systems enshrouded in dust, which absorbs most of their optical/UV emission and re-radiates it in the mid- and far-infrared. Radio observations are largely unaffected by dust obscuration, enabling us to study the central regions of LIRGs in an unbiased manner. The main goal of this project is to examine how the radio properties of local LIRGs relate to their infrared spectral characteristics. Here we present an analysis of the radio continuum properties of a subset of the Great Observatories All-sky LIRG Survey (GOALS), which consists of 202 nearby systems (z<0.088). Our radio sample consists of 35 systems, or 46 individual galaxies, that were observed at both 1.49 and 8.44 GHz with the VLA with a resolution of about 1 arcsec (FWHM). The aim of the project is to use the radio imagery to probe the central kpc of these LIRGs in search of active galactic nuclei. We used the archival data at 1.49 and 8.44 GHz to create radio-spectral-index maps using the standard relation between flux density Sv and frequency v, S~v^-a, where a is the radio spectral index. By studying the spatial variations in a, we classified the objects as radio-AGN, radio-SB, and AGN/SB (a mixture). We identified the presence of an active nucleus using the radio morphology, deviations from the radio/infrared correlation, and spatially resolved spectral index maps, and then correlated this to the usual mid-infrared ([NeV]/[NeII] and [OIV]/[NeII] line ratios and EQW of the 6.2 um PAH feature) and optical (BPT diagram) AGN diagnostics. We find that 21 out of the 46 objects in our sample are radio-AGN, 9 are classified as starbursts (SB), and 16 are AGN/SB. After comparing to other AGN diagnostics we find 3 objects out of the 46 that are identified as AGN based on the radio analysis, but are not classified as such based on the mid-infrared and optical AGN diagnostics presented in this study.Comment: 33 pages, 7 figures, 5 tables, to appear in A&

A Verilog-A Based Fractional Frequency Synthesizer Model for Fast and Accurate Noise Assessment

This paper presents a new strategy to simulate fractional frequency synthesizer behavioral models with better performance and reduced simulation time. The models are described in Verilog-A with accurate phase noise predictions and they are based on a time jitter to power spectral density transformation of the principal noise sources in a synthesizer. The results of a fractional frequency synthesizer simulation is compared with state of the art Verilog-A descriptions showing a reduction of nearly 20 times. In addition, experimental results of a fractional frequency synthesizer are compared to the simulation results to validate the proposed model

Draft Genome Sequence of a Multi-Metal Resistant Bacterium Pseudomonas putida ATH-43 Isolated from Greenwich Island, Antarctica

Indexación: Web of Science; Scopus.In this report we present the first draft genome sequence of a P. putida strain isolated from the Antarctic continent. The shotgun sequencing strategy, assembly, and subsequent annotation showed that the ATH-43 strain possesses a wide spectrum of genetic determinants involved in heavy metal and antibiotic resistance, apparently to cope with extreme oxidative stress conditions. P. putida ATH-43 genome now forms part of the 65 genomes of this species registered at the NCBI database (September, 2016) and it is highly related with the endophytic strain P. putida W619, which is also resistant to several heavy metals. Further characterization of multi-metal resistant psychrotrophic bacteria such as P. putida ATH-43 will be promising to develop novel strategies for heavy metal bioremediation in low temperature environments. All genome data has been submitted to NCBI.http://journal.frontiersin.org/article/10.3389/fmicb.2016.01777/ful

Forgotten Hispano-American Literature: Representation of Hispano-American Presses in Academic Libraries

As inclusion becomes a growing standard for universities in the United States, data extracted from OCLC suggest that university libraries in the United States build their Spanish-language collections with books purchased primarily in Spain and Mexico. This overlooks presses from 19 other Spanish-speaking countries in the Americas. This research is concerned with the representation of books published in these Hispano-American countries, and examines the holdings of 88 university libraries. The article discusses the drawbacks in neglecting purchase of literature published in Hispano-American countries, and the benefits of changing collection practices into a more inclusive design, including recommendations for best practices.</p