Quantifying TOLNet Ozone Lidar Accuracy During the 2014 DISCOVER-AQ and FRAPP Campaigns

The Tropospheric Ozone Lidar Network (TOLNet) is a unique network of lidar systems that measure high-resolution atmospheric profiles of ozone. The accurate characterization of these lidars is necessary to determine the uniformity of the network calibration. From July to August 2014, three lidars, the TROPospheric OZone (TROPOZ) lidar, the Tunable Optical Profiler for Aerosol and oZone (TOPAZ) lidar, and the Langley Mobile Ozone Lidar (LMOL), of TOLNet participated in the Deriving Information on Surface conditions from Column and Vertically Resolved Observations Relevant to Air Quality (DISCOVER-AQ) mission and the Front Range Air Pollution and Photochemistry xperiment (FRAPP) to measure ozone variations from the boundary layer to the top of the troposphere. This study presents the analysis of the intercomparison between the TROPOZ, TOPAZ, and LMOL lidars, along with comparisons between the lidars and other in situ ozone instruments including ozonesondes and a P-3B airborne chemiluminescence sensor. The TOLNet lidars measured vertical ozone structures with an accuracy generally better than 15 % within the troposphere. Larger differences occur at some individual altitudes in both the near-field and far-field range of the lidar systems, largely as expected. In terms of column average, the TOLNet lidars measured ozone with an accuracy better than 5 % for both the intercomparison between the lidars and between the lidars and other instruments. These results indicate that these three TOLNet lidars are suitable for use in air quality, satellite validation, and ozone modeling efforts

2016 Guidelines of the American Society of Mammalogists for the use of wild mammals in research and education.

Guidelines for use of wild mammal species in research are updated from Sikes et al. (2011). These guidelines cover current professional techniques and regulations involving the use of mammals in research and teaching; they also incorporate new resources, procedural summaries, and reporting requirements. Included are details on capturing, marking, housing, and humanely killing wild mammals. It is recommended that Institutional Animal Care and Use Committees (IACUCs), regulatory agencies, and investigators use these guidelines as a resource for protocols involving wild mammals, whether studied in the field or in captivity. These guidelines were prepared and approved by the American Society of Mammalogists (ASM), in consultation with professional veterinarians experienced in wildlife research and IACUCs, whose collective expertise provides a broad and comprehensive understanding of the biology of nondomesticated mammals. The current version of these guidelines and any subsequent modifications are available online on the Animal Care and Use Committee page of the ASM website (http://mammalogy.org/uploads/committee_files/CurrentGuidelines.pdf). Additional resources pertaining to the use of wild animals in research are available at: http://www.mammalsociety.org/committees/animal-care-and-use#tab3. Resumen—Los lineamientos para el uso de especies de mamíferos de vida silvestre en la investigación con base en Sikes et al. (2011) se actualizaron. Dichos lineamientos cubren técnicas y regulaciones rofesionales actuales que involucran el uso de mamíferos en la investigación y enseñanza; también incorporan recursos nuevos, resúmenes de procedimientos y requisitos para reportes. Se incluyen detalles acerca de captura, marcaje, manutención en cautiverio y eutanasia de mamíferos de vida silvestre. Se recomienda que los comités institucionales de uso y cuidado animal (cifras en inglés: IACUCs), las agencias reguladoras y los investigadores se adhieran a dichos lineamientos como fuente base de protocolos que involucren mamíferos de vida silvestre, ya sea investigaciones de campo o en cautiverio. Dichos lineamientos fueron preparados y aprobados por la ASM, en consulta con profesionales veterinarios experimentados en investigaciones de vida silvestre y IACUCS, de quienes cuya experiencia colectiva provee un entendimiento amplio y exhaustivo de la biología de mamíferos no-domesticados. La presente version de los lineamientos y modificaciones posteriores están disponibles en línea en la página web de la ASM, bajo Cuidado Animal y Comité de Uso: http://mammalogy.org/uploads/committee_files/CurrentGuidelines.pdf). Recursos adicionales relacionados con el uso de animales de vida silvestre para la investigación se encuentran disponibles en (http://www.mammalsociety.org/committees/animal-care-and-use#tab3)

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Microbiomes are vast communities of microorganisms and viruses that populate all natural ecosystems. Viruses have been considered to be the most variable component of microbiomes, as supported by virome surveys and examples of high genomic mosaicism. However, recent evidence suggests that the human gut virome is remarkably stable compared with that of other environments. Here, we investigate the origin, evolution and epidemiology of crAssphage, a widespread human gut virus. Through a global collaboration, we obtained DNA sequences of crAssphage from more than one-third of the world’s countries and showed that the phylogeography of crAssphage is locally clustered within countries, cities and individuals. We also found fully colinear crAssphage-like genomes in both Old-World and New-World primates, suggesting that the association of crAssphage with primates may be millions of years old. Finally, by exploiting a large cohort of more than 1,000 individuals, we tested whether crAssphage is associated with bacterial taxonomic groups of the gut microbiome, diverse human health parameters and a wide range of dietary factors. We identified strong correlations with different clades of bacteria that are related to Bacteroidetes and weak associations with several diet categories, but no significant association with health or disease. We conclude that crAssphage is a benign cosmopolitan virus that may have coevolved with the human lineage and is an integral part of the normal human gut virome

Myeloablative TMZ is required for efficacious immunotherapy against intracerebral tumor.

<p>Antitumor efficacy of a vaccination in the context of lymphopenia induced by the different TMZ regimens and the impact of these TMZ regimens as a single agent were investigated in wild-type C57BL/6 mice (n = 7) inoculated with an intracerebral injection of 5×10³ B16F10-OVA melanoma cells. These mice received vehicle, NMA or MA TMZ treatment followed by vaccine (A) or no vaccine (B). On day 3 after tumor implantation, dose-intensifying TMZ regimens were initiated and administered for 5 consecutive days intraperitoneally. Vaccinated mice received an intravenous adoptive transfer of 1×10⁷ splenocytes consisting of 1∶1 ratio of OT-I and C57BL/6 splenocytes on the day after termination of TMZ treatment. Mice underwent subsequent intradermal vaccination with 100 µg of SIINFEKL chicken ovalbumin epitope emulsified in CFA. (B) In order to assess the effects of TMZ alone, mice were also treated with TMZ in the absence of vaccine. Mice were monitored for morbidity end-points approved by the Duke University IACUC and sacrificed when end points were met. The experiment was performed three times. Survival analysis was performed using the Gehan-Breslow-Wilcoxon Test. Statistical significance was determined at a *p value ≤0.05.</p

Myeloablative TMZ enhances T-cell function yet IL-2 remains limiting.

<p>To compare the levels of IL-2 secretion by OT-I T-cells relative to IFNγ and TNFα levels in the context of NMA (A) and MA (B) TMZ regimens we performed CBA analysis. Splenocytes from mice receiving TMZ followed by OT-I transfer and vaccine, were harvested on day 7 after vaccination and cultured in the presence of 1 µM SIINFEKL chicken Ovalbumin epitope (cognate) or negative peptide control (non-cognate) for 72 hours in T-cell media alone. Supernatant was harvested and samples were subjected to to CBA analysis as specified by the manufacturer for murine IFNγ, TNFα and IL-2. Representative experiments are shown; experiments were performed in at least duplicate. Statistical analysis was performed using unpaired, two-tailed student’s t-tests. Statistical significance was determined at a *p value ≤0.05.</p

Myeloablative TMZ leads to elevated IL-2 serum levels, which are required for optimal antigen-specific T-cell expansion.

<p>The presence and requirement of endogenous IL-2 serum levels for optimal antigen-specific T-cell expansion following myeloablative TMZ was evaluated in wild-type C57BL/6 mice (n = 5 per group). To investigate the levels of endogenous IL-2, mice were treated with vehicle, NMA or MA TMZ for 5 consecutive days. Myeloablated mice received an HSC rescue on the day after cessation of TMZ treatment. (A) Serum IL-2 levels were analyzed 5 days after cessation of TMZ treatment by LINCOplex analysis. Statistical analysis was performed using Mann-Whitney test. Statistical significance was determined at a *p value ≤0.05. (B) To assess the role of IL-2 in potentiating antigen-specific T-cell responses, mice were infused with anti-IL-2 antibodies (S4B6 and JES6-1,250 µg per mouse, intraperitoneal), followed by OT-I ALT transfer and peptide vaccine in CFA. Anti-IL-2 antibodies were administered every other day for 7 doses. Mice were bled on day 7 and blood was stained with anti-CD8 and OVA tetramer w\as described before on <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059082#pone-0059082-g003" target="_blank">Figure 3</a>. Absolute numbers per µl of blood were calculated using Flowcount^® beads from Beckman Coulter^©. Statistical analysis was performed using unpaired t- test. Statistical significance was determined at a *p value ≤0.05.</p

Myeloablative TMZ results in protracted depletion of CD4⁺Foxp3⁺

<p><b>T cells.</b> To evaluate, the impact of different TMZ regimens on CD4⁺Foxp3⁺ T_Regs C57BL/6 mice (n = 5) were treated with vehicle, NMA or MA TMZ regimens as stated before in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0059082#pone-0059082-g001" target="_blank">Figure 1</a>. Mice were bled retro-orbitally on days 2, 7, 14 and 28 after termination of TMZ administration and submitted to flow cytometry analysis. Immediate effects of TMZ on CD4⁺Foxp3⁺ T_Regs (A), on day 2 and the recovery kinetics over time are shown (B). Absolute numbers per microliter of blood were calculated using Flowcount^® beads from Beckman Coulter^©. Representative experiments are shown; all experiments were performed in at least duplicate. Statistical analysis was performed using Mann-Whitney test. Statistical significance was determined at a *p value ≤0.05.</p

Data from: Early bursts of body size and shape evolution are rare in comparative data

George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early-burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long-term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data

Data from: Early bursts of body size and shape evolution are rare in comparative data

George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations—more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early-burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long-term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data