title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1235 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Oxidative stress and antioxidants in the trabecular meshwork link: https://peerj.com/articles/8121 last-modified: 2019-11-26 description: Glaucoma is an age-dependent disease closely related to oxidative stress and is regarded as the second leading cause of irreversible blindness worldwide. In recent years, many studies have shown that morphological and functional abnormalities of the trabecular meshwork (TM) are closely related to glaucoma, especially with respect to oxidative stress. In this review, the mechanisms of oxidative stress in the TM and treatment strategies for this condition, including strategies involving antioxidants, noncoding RNAs and exogenous compounds, are discussed. Although many questions remain to be answered, the reviewed findings provide insights for further research on oxidative stress alleviation in glaucoma and suggest new targets for glaucoma prevention. creator: Mingxuan Wang creator: Yajuan Zheng uri: https://doi.org/10.7717/peerj.8121 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang and Zheng title: Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia link: https://peerj.com/articles/8144 last-modified: 2019-11-26 description: The best facultative anaerobes among vertebrates are members of the genera Trachemys (pond slider turtles) and Chrysemys (painted turtles), and are able to survive without oxygen for up to 12 to 18 weeks at ∼3 °C. In this study, we utilized RNAseq to profile the transcriptomic changes that take place in response to 20 hrs of anoxia at 5 °C in the liver of the red eared slide turtle (Trachemys scripta elegans). Sequencing reads were obtained from at least 18,169 different genes and represented a minimum 49x coverage of the C. picta bellii exome. A total of 3,105 genes showed statistically significant changes in gene expression between the two animal groups, of which 971 also exhibited a fold change equal to or greater than 50% of control normoxic values. This study also highlights a number of anoxia-responsive molecular pathways that are may be important to navigating anoxia survival. These pathways were enriched in mRNA found to significantly increase in response to anoxia and included molecular processes such as DNA damage repair and metabolic reprogramming. For example, our results indicate that the anoxic turtle may utilize succinate metabolism to yield a molecule of GTP in addition to the two molecules that results from lactate production, and agrees with other established models of anoxia tolerance. Collectively, our analysis provides a snapshot of the molecular landscape of the anoxic turtle and may provide hints into the how this animal is capable of surviving this extreme environmental stress. creator: Kyle K. Biggar creator: Jing Zhang creator: Kenneth B. Storey uri: https://doi.org/10.7717/peerj.8144 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Biggar et al. title: Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.) link: https://peerj.com/articles/7929 last-modified: 2019-11-25 description: The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species. creator: Xin Hu creator: Lili Zhu creator: Yi Zhang creator: Li Xu creator: Na Li creator: Xingguo Zhang creator: Yu Pan uri: https://doi.org/10.7717/peerj.7929 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hu et al. title: Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications link: https://peerj.com/articles/8033 last-modified: 2019-11-25 description: The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong. creator: Siuli Mitra creator: Vaishnavi Kunteepuram creator: Klaus-Peter Koepfli creator: Neha Mehra creator: Wajeeda Tabasum creator: Ara Sreenivas creator: Ajay Gaur uri: https://doi.org/10.7717/peerj.8033 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mitra et al. title: Assessment of North American arthropod collections: prospects and challenges for addressing biodiversity research link: https://peerj.com/articles/8086 last-modified: 2019-11-25 description: Over 300 million arthropod specimens are housed in North American natural history collections. These collections represent a “vast hidden treasure trove” of biodiversity −95% of the specimen label data have yet to be transcribed for research, and less than 2% of the specimens have been imaged. Specimen labels contain crucial information to determine species distributions over time and are essential for understanding patterns of ecology and evolution, which will help assess the growing biodiversity crisis driven by global change impacts. Specimen images offer indispensable insight and data for analyses of traits, and ecological and phylogenetic patterns of biodiversity. Here, we review North American arthropod collections using two key metrics, specimen holdings and digitization efforts, to assess the potential for collections to provide needed biodiversity data. We include data from 223 arthropod collections in North America, with an emphasis on the United States. Our specific findings are as follows: (1) The majority of North American natural history collections (88%) and specimens (89%) are located in the United States. Canada has comparable holdings to the United States relative to its estimated biodiversity. Mexico has made the furthest progress in terms of digitization, but its specimen holdings should be increased to reflect the estimated higher Mexican arthropod diversity. The proportion of North American collections that has been digitized, and the number of digital records available per species, are both much lower for arthropods when compared to chordates and plants. (2) The National Science Foundation’s decade-long ADBC program (Advancing Digitization of Biological Collections) has been transformational in promoting arthropod digitization. However, even if this program became permanent, at current rates, by the year 2050 only 38% of the existing arthropod specimens would be digitized, and less than 1% would have associated digital images. (3) The number of specimens in collections has increased by approximately 1% per year over the past 30 years. We propose that this rate of increase is insufficient to provide enough data to address biodiversity research needs, and that arthropod collections should aim to triple their rate of new specimen acquisition. (4) The collections we surveyed in the United States vary broadly in a number of indicators. Collectively, there is depth and breadth, with smaller collections providing regional depth and larger collections providing greater global coverage. (5) Increased coordination across museums is needed for digitization efforts to target taxa for research and conservation goals and address long-term data needs. Two key recommendations emerge: collections should significantly increase both their specimen holdings and their digitization efforts to empower continental and global biodiversity data pipelines, and stimulate downstream research. creator: Neil S. Cobb creator: Lawrence F. Gall creator: Jennifer M. Zaspel creator: Nicolas J. Dowdy creator: Lindsie M. McCabe creator: Akito Y. Kawahara uri: https://doi.org/10.7717/peerj.8086 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cobb et al. title: Visible and near-infrared radiation may be transmitted or absorbed differently by beetle elytra according to habitat preference link: https://peerj.com/articles/8104 last-modified: 2019-11-25 description: BackgroundThe exoskeleton of an insect could be an important factor in the success of its evolutionary process. This reaches its maximum expression in beetles, which constitute the most diversified animal taxon. The involvement in the management of environmental radiation could be one of the most important functions of the exoskeleton due to the passive contributions to the thermoregulation of body temperature. We study whether the elytra of two sympatric and closely related beetle species respond differentially to the radiation of distinct wavelengths in agreement with their ecological preferences.MethodsOnthophagus coenobita (Herbst) and O. medius (Kugelaan) occupy different habitats and environmental conditions (shaded vs. unshaded from solar radiation). The potential adaptive variations to thermoregulation under these different ecological conditions were studied using the responses of their exoskeletons to radiation of different wavelengths (ultraviolet, visible and near-infrared). For these two species, the amounts of the three wavelengths that were reflected, transmitted or absorbed by the exoskeleton were measured using of a spectrophotometer. In addition, the darkness and thickness of the elytra were examined to determine whether these two features influence the management of radiation by the exoskeleton.ResultsBoth species differ in the management of visible and near-infrared radiation. In agreement with habitat preferences, the species inhabiting shaded conditions would allow infrared and visible radiation to penetrate the elytra more easily to heat internal body parts, while the elytra of the heliophilous species would have increased absorbance of these same types of radiation. An increase in body size (and therefore in elytron thickness) and the quantity of dark spots may serve as barriers against exogenous heat gain. However, the maintenance of between-species differences independent of the effects of these two morphological features led us to suspect that an unconsidered elytron characteristic may also be affecting these differences.DiscussionThe results of the involvement of the exoskeleton thickness and spots in the thermoregulation of insects opens new research lines to obtain a better understanding of the function of the exoskeleton as a passive thermoregulation mechanism in Coleoptera. creator: Eva Cuesta creator: Jorge M. Lobo uri: https://doi.org/10.7717/peerj.8104 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cuesta and Lobo title: Familiarity with visual stimuli boosts recency bias in macaques link: https://peerj.com/articles/8105 last-modified: 2019-11-25 description: To probe how non-human primates (NHPs) decode temporal dynamic stimuli, we used a two-alternative forced choice task (2AFC), where the cue was dynamic: a movie snippet drawn from an animation that transforms one image into another. When the cue was drawn from either the beginning or end of the animation, thus heavily weighted towards one (the target) of both images (the choice pair), then primates performed at high levels of accuracy. For a subset of trials, however, the cue was ambiguous, drawn from the middle of the animation, containing information that could be associated to either image. Those trials, rewarded randomly and independent of choice, offered an opportunity to study the strategy the animals used trying to decode the cue. Despite being ambiguous, the primates exhibited a clear strategy, suggesting they were not aware that reward was given non-differentially. More specifically, they relied more on information provided at the end than at the beginning of those cues, consistent with the recency effect reported by numerous serial position studies. Interestingly and counterintuitively, this effect became stronger for sessions where the primates were already familiar with the stimuli. In other words, despite having rehearsed with the same stimuli in a previous session, the animals relied even more on a decision strategy that did not yield any benefits during a previous session. In the discussion section we speculate on what might cause this behavioral shift towards stronger bias, as well as why this behavior shows similarities with a repetition bias in humans known as the illusory truth effect. creator: Nicolas Brunet creator: Bharathi Jagadeesh uri: https://doi.org/10.7717/peerj.8105 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Brunet and Jagadeesh title: Computer-aided simulation and exergy analysis of TiO2 nanoparticles production via green chemistry link: https://peerj.com/articles/8113 last-modified: 2019-11-25 description: BackgroundThe production of photocatalytic nanoparticles such as TiO2 has received increasing interest for biomedical and wastewater treatment applications. However, the conventional synthesis of such materials faces several environmental concerns.MethodsIn this work, green synthesis is addressed to prepare TiO2 nanoparticles at large scale using Lemongrass (Cymbopogon citratus) and titanium isopropoxide (TTIP). This process was designed and modeled using computer-aided process engineering (CAPE) in order to obtain the extended mass/energy balances, as well as operating parameters. Process simulation was carried out using the commercial software Aspen Plus®. In addition, energy performance of large-scale nanoparticle production was analyzed to identify alternatives for process improvement from an exergetic point of view.ResultsThe production capacity of the plant was estimated as 1,496 t/y of TiO2 nanoparticles by the conversion of 32,675 t/y lemongrass and 5,724 t/y TTIP. Hence, the overall production yield is 0.26 kg TiO2/kg TTIP. Exergy analysis reported an overall exergy efficiency of 0.27% and an exergy loss of 159,824.80 MJ/h. These results suggest that such a process requires the implementation of process improvement strategies to reach a more sustainable design from energy and thermodynamic viewpoints. creator: Samir Meramo-Hurtado creator: Kariana Moreno-Sader creator: Ángel D. González-Delgado uri: https://doi.org/10.7717/peerj.8113 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Meramo-Hurtado et al. title: Application of open field, tonic immobility, and attention bias tests to hens with different ranging patterns link: https://peerj.com/articles/8122 last-modified: 2019-11-25 description: Assessment of negative affective states is a key component of animal welfare research. In laying hens, excessive fearfulness results in reduced production and increased sensitivity to stress. Fearfulness can be defined as a response to a known threat, but anxiety is a response to an unknown threat and may have similar negative consequences. The open field test and tonic immobility test are commonly applied to measure fearfulness in laying hens. An attention bias test that measured individual hen’s responses to playback of a conspecific alarm call in the presence of food was recently pharmacologically validated using an anxiogenic drug but was confounded by the hen’s typical motionless response in a novel environment. The current study used 56-week old free-range layers to further assess the validity of an attention bias test to differentiate ranging treatment groups in comparison with the open field and tonic immobility tests. The selected hens varied in their range use patterns as tracked by radio-frequency identification technology. ‘Indoor’ hens did not access the range and ‘outdoor’ hens ranged daily; previous research has confirmed higher fearfulness in hens that remain indoors. The tonic immobility test did not differentiate ranging groups (P = 0.34), but indoor birds were slower to first step (P = 0.03) and stepped less (P = 0.02) in the open field test. The attention bias test occurred in an isolated wooden box using a conspecific alarm call playback (a threat) and mixed grain (a positive stimulus). The behavioural response of latency to resume eating following playback of the alarm call was measured to differentiate the anxiety states of the indoor and outdoor ranging birds. Before the attention bias test could occur, birds had to be habituated to the test box across three separate 5-minute sessions to increase the willingness to feed within the novel test environment. All birds ate faster across time (P < 0.001) but the indoor birds were slower to eat than the outdoor birds (P < 0.001). In this study, the latency to resume eating following an alarm call was determined to be a poor measure for highly anxious birds as they failed to eat at all. Forty-six percent of indoor hens were excluded for not eating across the 5-minute test. Of the birds that did eat, only 7% of indoor hens ate following playback of the alarm call, compared with 36% of outdoor hens. This repetition of an attention bias test for laying hens highlights the challenges in assessing hens with extreme fearful/anxious responses and that information may be missed when non-performing hens are excluded from behavioural tests. We suggest that latency to eat in a novel arena without any alarm call playback is an informative measure of anxious state that can be applied to all hens but consideration must be made of potential differences in food motivation. creator: Dana L.M. Campbell creator: Emily J. Dickson creator: Caroline Lee uri: https://doi.org/10.7717/peerj.8122 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Campbell et al. title: Introducing a new tool to navigate, understand and use International Codes of Nomenclature link: https://peerj.com/articles/8127 last-modified: 2019-11-25 description: BackgroundIn order to designate the various concepts of taxa in biology, evolution and paleontology, scientists have developed various rules on how to create unique names for taxa. Different Codes of Nomenclature have been developed for animals, plants, fungi, bacteria etc., with standard sets of Rules that govern the formation, publication and application of the nomina of extant and extinct species. These Codes are the result of decades of discussions, workshops, publications and revisions. The structure and complexity of these Codes have been criticized many times by zoologists. This project aims, using the International Code of Zoological Nomenclature as a case study, to show that the structure of these Codes is better reflected and understood as networks.MethodsThe majority of the text of the Code has been divided into hundreds of Nodes of different types, connected to each other with different types of Edges to form a network. The various mathematical descriptors of the entire system, as well as for the elements of the network, have been conceptually framed to help describing and understanding the Code as a network.ResultsThe network of the Code comprises 1,379 Nodes, which are connected with 11,276 Edges. The structure of the Code can be accurately described as a network, a mathematical structure that is better suited than any kind of linear text publication to reflect its structure.DiscussionThinking of the Code as a network allows a better, in-depth understanding of the Code itself, as the user can navigate in a more efficient way, as well as to depict and analyze all the implied connections between the various parts of the Code that are not visible immediately. The network of the Code is an open access tool that could also help teaching, using and disseminating the Code. More importantly, this network is a powerful tool that allows identifying a priori the parts of the Code that could be potentially affected by upcoming amendment and revisions. This kind of analysis is not limited to nomenclature, as it could be applied to other fields that use complex textbooks with long editing history, such as Law, Medicine and Linguistics. creator: Evangelos Vlachos uri: https://doi.org/10.7717/peerj.8127 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Vlachos