title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1678 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A systematic review of differential rate of use of the word “evolve” across fields link: https://peerj.com/articles/3639 last-modified: 2017-08-21 description: BackgroundAlthough evolution is the driving force behind many of today’s major public health and agriculture issues, both journalists and scientific researchers often do not use the term “evolve” in discussions of these topics.MethodsIn a total of 1,066 articles and 716 papers selected from 25 US newspapers and 34 scientific journals, we assess usage of the word “evolve” and its substitute words in the contexts of cancer tumor drug resistance, HIV drug resistance, mosquito insecticide resistance, and weed pesticide resistance.ResultsWe find significant differences in the use of “evolve” among fields and sources. “Evolve” is used most when discussing weed pesticide resistance (25.9% in newspapers, 52.4% in journals) and least when discussing cancer tumor drug resistance (3.9% in newspapers, 9.8% in journals). On average, scientific journals use “evolve” more often (22.2%) than newspapers (7.8%). Different types of journals (general science, general clinical, cancer specific, and drug resistance specific) show significantly different “evolve” usages when discussing cancer tumor drug resistance.DiscussionWe examine potential explanations of these findings, such as the relatively recent framing of cancer in evolutionary terms, before looking at consequences of low “evolve” usage and of differential “evolve” usage across fields. Use of the word “evolve” may not reflect current understanding of the problems we examine. However, given that our ability to tackle resistance issues relies upon accurate understandings of what causes and exacerbates resistance, use of the word “evolve” when called for may help us confront these issues in the future. creator: Nina Singh creator: Matthew T. Sit creator: Marissa K. Schutte creator: Gabriel E. Chan creator: Jeyson E. Aldana creator: Diana Cervantes creator: Clyde H. Himmelstein creator: Pamela J. Yeh uri: https://doi.org/10.7717/peerj.3639 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Singh et al. title: RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers link: https://peerj.com/articles/3631 last-modified: 2017-08-21 description: Identification of appropriate reference genes (RGs) is critical to accurate data interpretation in quantitative real-time PCR (qPCR) experiments. In this study, we have utilised next generation RNA sequencing (RNA-seq) to analyse the transcriptome of a panel of non-melanoma skin cancer lesions, identifying genes that are consistently expressed across all samples. Genes encoding ribosomal proteins were amongst the most stable in this dataset. Validation of this RNA-seq data was examined using qPCR to confirm the suitability of a set of highly stable genes for use as qPCR RGs. These genes will provide a valuable resource for the normalisation of qPCR data for the analysis of non-melanoma skin cancer. creator: Van L.T. Hoang creator: Lisa N. Tom creator: Xiu-Cheng Quek creator: Jean-Marie Tan creator: Elizabeth J. Payne creator: Lynlee L. Lin creator: Sudipta Sinnya creator: Anthony P. Raphael creator: Duncan Lambie creator: Ian H. Frazer creator: Marcel E. Dinger creator: H. Peter Soyer creator: Tarl W. Prow uri: https://doi.org/10.7717/peerj.3631 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Hoang et al. title: Implications of nutritional stress as nestling or fledgling on subsequent attractiveness and fecundity in zebra finches (Taeniopygia guttata) link: https://peerj.com/articles/3628 last-modified: 2017-08-21 description: The conditions an organism experiences during early development can have profound and long lasting effects on its subsequent behavior, attractiveness, and life history decisions. Most previous studies have exposed individuals to different conditions throughout development until nutritional independence. Yet under natural conditions, individuals may experience limitations for much shorter periods due to transient environmental fluctuations. Here, we used zebra finches (Taeniopygia guttata) in captivity to determine if conditions experienced during distinctly different early developmental phases contribute differently to male and female attractiveness and subsequent reproduction. We conducted a breeding experiment in which offspring were exposed to food regimes with (a) low quality food provided only during the nestling period, (b) low quality food provided only during the fledgling period, or (c) high quality food throughout early development. We show that despite short-term effects on biometry and physiology, there were no effects on either male or female attractiveness, as tested in two-way mate choice free-flight aviary experiments. In a subsequent breeding experiment, the offspring from the initial experiment were allowed to breed themselves. The next generation offspring from mothers raised under lower quality nutrition as either nestling or fledging were lighter at hatching compared to offspring from mothers raised under higher quality nutrition whereas paternal early nutrition had no such effects. The lack of early developmental limitations on attractiveness suggests that attractiveness traits were not affected or that birds compensated for any such effects. Furthermore, maternal trans-generational effects of dietary restrictions emphasize the importance of role of limited periods of early developmental stress in the expression of environmentally determined fitness components. creator: Mariam Honarmand creator: E. Tobias Krause creator: Marc Naguib uri: https://doi.org/10.7717/peerj.3628 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Honarmand et al. title: Influence of CNTRENE® C100LM carbon nanotube material on the growth and regulation of Escherichia coli link: https://peerj.com/articles/3721 last-modified: 2017-08-18 description: The growing use of carbon nanotubes (CNTs) in industrial and consumer products raises important questions about their environmental fate and impact on prokaryotes. In the environment, CNTs are exposed to a variety of conditions (e.g., UV light) that could lead to decomposition and changes in their chemical properties. Therefore, the potential cytotoxic effect of both pristine and artificially aged carboxyl functionalized CNTRENE® C100LM CNTmaterial at neutral and acidic conditions on Escherichia coli K12 was analyzed using a minimal inhibitory concentration (MIC) assay, which also allowed monitoring of non-lethal growth effects. However, there were no observable MIC or significant changes in growth behavior in E. coli K12 when exposed to pristine or aged CNTs. Exposure to pristine CNTRENE® C100LM CNT material did not appear to influence cell morphology or damage the cells when examined by electron microscopy. In addition, RNA sequencing revealed no observable regulatory changes in typical stress response pathways. This is surprising considering that previous studies have claimed high cytotoxicity of CNTs, including carboxyl functionalized single-walled CNTs, and suggest that other factors such as trace heavy metals or other impurities are likely responsible for many of the previously reported cytotoxicity in E. coli and possibly other microorganisms. creator: Brittany Twibell creator: Kalie Somerville creator: Geoffrey Manani creator: Molly Duszynski creator: Adam Wanekaya creator: Paul Schweiger uri: https://doi.org/10.7717/peerj.3721 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Twibell et al. title: Exposure to elevated sea-surface temperatures below the bleaching threshold impairs coral recovery and regeneration following injury link: https://peerj.com/articles/3719 last-modified: 2017-08-18 description: Elevated sea surface temperatures (SSTs) are linked to an increase in the frequency and severity of bleaching events due to temperatures exceeding corals’ upper thermal limits. The temperatures at which a breakdown of the coral-Symbiodinium endosymbiosis (coral bleaching) occurs are referred to as the upper thermal limits for the coral species. This breakdown of the endosymbiosis results in a reduction of corals’ nutritional uptake, growth, and tissue integrity. Periods of elevated sea surface temperature, thermal stress and coral bleaching are also linked to increased disease susceptibility and an increased frequency of storms which cause injury and physical damage to corals. Herein we aimed to determine the capacity of corals to regenerate and recover from injuries (removal of apical tips) sustained during periods of elevated sea surface temperatures which result in coral stress responses, but which do not result in coral bleaching (i.e., sub-bleaching thermal stress events). In this study, exposure of the species Acropora aspera to an elevated SST of 32 °C (2 °C below the bleaching threshold, 34 °C) was found to result in reduced fluorescence of green fluorescent protein (GFP), reduced skeletal calcification and a lack of branch regrowth at the site of injury, compared to corals maintained under ambient SST conditions (26 °C). Corals maintained under normal, ambient, sea surface temperatures expressed high GFP fluorescence at the injury site, underwent a rapid regeneration of the coral branch apical tip within 12 days of sustaining injury, and showed extensive regrowth of the coral skeleton. Taken together, our results have demonstrated that periods of sustained increased sea surface temperatures, below the corals’ bleaching threshold but above long-term summertime averages, impair coral recovery from damage, regardless of the onset or occurrence of coral bleaching. creator: Joshua Louis Bonesso creator: William Leggat creator: Tracy Danielle Ainsworth uri: https://doi.org/10.7717/peerj.3719 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Bonesso et al. title: Inadequate thermal refuge constrains landscape habitability for a grassland bird species link: https://peerj.com/articles/3709 last-modified: 2017-08-18 description: Ecologists have long recognized the influence that environmental conditions have on abundance and range extent of animal species. We used the northern bobwhite (Colinus virginianus; hereafter bobwhite) as a model species for studying how microclimates serve as refuge against severe weather conditions. This species serves as an indicator or umbrella species for other sensitive ground-nesting, grassland obligate species. We conducted a mensurative field experiment in the rolling plains of Texas, USA, a semi-arid ecosystem on the southwestern periphery of bobwhite range, to determine whether native bunch grasses, apparently suitable for bobwhite nesting, could reduce ambient temperature below levels harmful for eggs. During the nesting season, we compared temperature and relative humidity readings at daily heat maxima (i.e., the 3 h during each day with highest temperatures) during the nesting season over the course of two years at 63 suitable nest sites paired with 63 random locations (n = 126) using two sensors at ∼10 and ∼60 cm above ground level. Mean temperature at nest height was 2.3% cooler at nest sites (35.99 °C ± 0.07 SE) compared to random locations (36.81 °C ± 0.07 SE); at ambient height, nest sites were slightly cooler (32.78 °C ± 0.06 SE) than random location (32.99 °C ± 0.06 SE). Mean relative humidity at nest sites was greater at nest height (34.53% ± 0.112 SE) and ambient height (36.22% ± 0.10 SE) compared to random locations at nest (33.35% ± 0.12 SE) and ambient height (35.75% ± 0.10 SE). Based on these results, cover at sites that appear visually suitable for nesting by bobwhites and other ground nesting birds provided adequate thermal refuge in the rolling plains by maintaining cooler, moister microclimates than surrounding non-nesting locations. Post-hoc analyses of data revealed that habitat conditions surrounding suitable nest sites strongly influenced thermal suitability of the substrate. Given that eggs of bobwhites and probably other species would experience lethal temperatures without these thermal refuges in the context of proper habitat condition, nesting vegetation is a critical component of niche space for bobwhites and other ground nesting birds in semi-arid regions. Many contemporary land uses, however, degrade or destroy bunch grasses and grassland systems, and thus decrease landscape inhabitability. Conservationists working with obligate grassland species that require bunch grasses in semi-arid regions should develop land management strategies that maximize the availability of these thermal refuges across space and time. creator: John M. Tomecek creator: Brian L. Pierce creator: Kelly S. Reyna creator: Markus J. Peterson uri: https://doi.org/10.7717/peerj.3709 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2017 Tomecek et al. title: Genomic evidence of bitter taste in snakes and phylogenetic analysis of bitter taste receptor genes in reptiles link: https://peerj.com/articles/3708 last-modified: 2017-08-18 description: As nontraditional model organisms with extreme physiological and morphological phenotypes, snakes are believed to possess an inferior taste system. However, the bitter taste sensation is essential to distinguish the nutritious and poisonous food resources and the genomic evidence of bitter taste in snakes is largely scarce. To explore the genetic basis of the bitter taste of snakes and characterize the evolution of bitter taste receptor genes (Tas2rs) in reptiles, we identified Tas2r genes in 19 genomes (species) corresponding to three orders of non-avian reptiles. Our results indicated contractions of Tas2r gene repertoires in snakes, however dramatic gene expansions have occurred in lizards. Phylogenetic analysis of the Tas2rs with NJ and BI methods revealed that Tas2r genes of snake species formed two clades, whereas in lizards the Tas2r genes clustered into two monophyletic clades and four large clades. Evolutionary changes (birth and death) of intact Tas2r genes in reptiles were determined by reconciliation analysis. Additionally, the taste signaling pathway calcium homeostasis modulator 1 (Calhm1) gene of snakes was putatively functional, suggesting that snakes still possess bitter taste sensation. Furthermore, Phylogenetically Independent Contrasts (PIC) analyses reviewed a significant correlation between the number of Tas2r genes and the amount of potential toxins in reptilian diets, suggesting that insectivores such as some lizards may require more Tas2rs genes than omnivorous and carnivorous reptiles. creator: Huaming Zhong creator: Shuai Shang creator: Xiaoyang Wu creator: Jun Chen creator: Wanchao Zhu creator: Jiakuo Yan creator: Haotian Li creator: Honghai Zhang uri: https://doi.org/10.7717/peerj.3708 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Zhong et al. title: Extended exposure to elevated temperature affects escape response behaviour in coral reef fishes link: https://peerj.com/articles/3652 last-modified: 2017-08-18 description: The threat of predation, and the prey’s response, are important drivers of community dynamics. Yet environmental temperature can have a significant effect on predation avoidance techniques such as fast-start performance observed in marine fishes. While it is known that temperature increases can influence performance and behaviour in the short-term, little is known about how species respond to extended exposure during development. We produced a startle response in two species of damselfish, the lemon damsel Pomacentrus moluccensis, and the Ambon damselfish Pomacentrus amboinensis, by the repeated use of a drop stimulus. We show that the length of thermal exposure of juveniles to elevated temperature significantly affects this escape responses. Short-term (4d) exposure to warmer temperature affected directionality and responsiveness for both species. After long-term (90d) exposure, only P. moluccensis showed beneficial plasticity, with directionality returning to control levels. Responsiveness also decreased in both species, possibly to compensate for higher temperatures. There was no effect of temperature or length of exposure on latency to react, maximum swimming speed, or escape distance suggesting that the physical ability to escape was maintained. Evidence suggests that elevated temperature may impact some fish species through its effect on the behavioural responses while under threat rather than having a direct influence on their physical ability to perform an effective escape response. creator: Donald T. Warren creator: Jennifer M. Donelson creator: Mark I. McCormick uri: https://doi.org/10.7717/peerj.3652 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 Warren et al. title: Shifting communities after­­ typhoon damage on an upper mesophotic reef in Okinawa, Japan link: https://peerj.com/articles/3573 last-modified: 2017-08-18 description: Very few studies have been conducted on the long-term effects of typhoon damage on mesophotic coral reefs. This study investigates the long-term community dynamics of damage from Typhoon 17 (Jelawat) in 2012 on the coral community of the upper mesophotic Ryugu Reef in Okinawa, Japan. A shift from foliose to bushy coral morphologies between December 2012 and August 2015 was documented, especially on the area of the reef that was previously recorded to be poor in scleractinian genera diversity and dominated by foliose corals. Comparatively, an area with higher diversity of scleractinian coral genera was observed to be less affected by typhoon damage with more stable community structure due to less change in dominant coral morphologies. Despite some changes in the composition of dominant genera, the generally high coverage of the mesophotic coral community is facilitating the recovery of Ryugu Reef after typhoon damage. creator: Kristine N. White creator: David K. Weinstein creator: Taku Ohara creator: Vianney Denis creator: Javier Montenegro creator: James D. Reimer uri: https://doi.org/10.7717/peerj.3573 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2017 White et al. title: Lionfish (Pterois spp.) invade the upper-bathyal zone in the western Atlantic link: https://peerj.com/articles/3683 last-modified: 2017-08-17 description: Non-native lionfish have been recorded throughout the western Atlantic on both shallow and mesophotic reefs, where they have been linked to declines in reef health. In this study we report the first lionfish observations from the deep sea (>200 m) in Bermuda and Roatan, Honduras, with lionfish observed to a maximum depth of 304 m off the Bermuda platform, and 250 m off West End, Roatan. Placed in the context of other deeper lionfish observations and records, our results imply that lionfish may be present in the 200–300 m depth range of the upper-bathyal zone across many locations in the western Atlantic, but currently are under-sampled compared to shallow habitats. We highlight the need for considering deep-sea lionfish populations in future invasive lionfish management. creator: Erika Gress creator: Dominic A. Andradi-Brown creator: Lucy Woodall creator: Pamela J. Schofield creator: Karl Stanley creator: Alex D. Rogers uri: https://doi.org/10.7717/peerj.3683 license: http://creativecommons.org/publicdomain/zero/1.0/ rights: