title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1337 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Recently-adopted foraging strategies constrain early chick development in a coastal breeding gull link: https://peerj.com/articles/7250 last-modified: 2019-07-10 description: Human-mediated food sources offer possibilities for novel foraging strategies by opportunistic species. Yet, relative costs and benefits of alternative foraging strategies vary with the abundance, accessibility, predictability and nutritional value of anthropogenic food sources. The extent to which such strategies may ultimately alter fitness, can have important consequences for long-term population dynamics. Here, we studied the relationships between parental diet and early development in free-ranging, cross-fostered chicks and in captive-held, hand-raised chicks of Lesser Black-backed Gulls (Larus fuscus) breeding along the Belgian coast. This traditionally marine and intertidal foraging species is now increasingly taking advantage of human activities by foraging on terrestrial food sources in agricultural and urban environments. In accordance with such behavior, the proportion of terrestrial food in the diet of free-ranging chicks ranged between 4% and 80%, and consistent stable isotope signatures between age classes indicated that this variation was mainly due to between-parent variation in feeding strategies. A stronger terrestrial food signature in free-ranging chicks corresponded with slower chick development. However, no consistent differences in chick development were found when contrasting terrestrial and marine diets were provided ad libitum to hand-raised chicks. Results of this study hence suggest that terrestrial diets may lower reproductive success due to limitations in food quantity, rather than quality. Recent foraging niche expansion toward terrestrial resources may thus constitute a suboptimal alternative strategy to marine foraging for breeding Lesser Black-backed Gulls during the chick-rearing period. creator: Alejandro Sotillo creator: Jan M. Baert creator: Wendt Müller creator: Eric W.M. Stienen creator: Amadeu M.V.M. Soares creator: Luc Lens uri: https://doi.org/10.7717/peerj.7250 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Sotillo et al. title: Comparative transcriptomic and proteomic analyses of the green and white parts of chimeric leaves in Ananas comosus var. bracteatus link: https://peerj.com/articles/7261 last-modified: 2019-07-10 description: BackgroundAnanas comosus var. bracteatus has high ornamental value due to its chimeric leaves. However, the chimeric trait is very unstable in red pineapple plants, and transcriptional variation between the two types of cells (white/green cells) and the molecular mechanism responsible for their albino phenotype remain poorly understood.MethodsComparative transcriptomic and proteomic analyses of the white parts (Whs) and green parts (Grs) of chimeric leaves were performed.ResultsIn total, 1,685 differentially expressed genes (DEGs) (712 upregulated and 973 downregulated) and 1,813 differentially abundant proteins (DAPs) (1,018 with low abundance and 795 with high abundance) were identified. Based on Gene Ontology (Go) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, the DEGs were mostly involved in carbon fixation in photosynthetic organisms, porphyrin and chlorophyll metabolism and oxidative phosphorylation, while proteomic analysis revealed that DAPs were mostly related to ribosomes, photosynthesis, photosynthesis antennas, and porphyrin and chlorophyll metabolism. Combined analysis showed increased mRNA levels but low abundance of nine proteins level in Whs /Grs related to photosynthetic pigment and photosynthesis. Transcriptional changes, posttranscriptional regulation and translational alterations of key enzymes involved in chlorophyll biosynthesis and photosynthesis may play important roles in the albino parts of chimeric leaves. creator: Yanbin Xue creator: Jun Ma creator: Yehua He creator: Sanmiao Yu creator: Zhen Lin creator: Yingyuan Xiong creator: Fatima Rafique creator: Fuxing Jiang creator: Lingxia Sun creator: Mingdong Ma creator: Yujue Zhou creator: Xi Li creator: Zhuo Huang uri: https://doi.org/10.7717/peerj.7261 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xue et al. title: Towards sex identification of Asian Palmyra palm (Borassus flabellifer L.) by DNA fingerprinting, suppression subtractive hybridization and de novo transcriptome sequencing link: https://peerj.com/articles/7268 last-modified: 2019-07-10 description: BackgroundAsian Palmyra palm, the source of palm-sugar, is dioecious with a long juvenile period requiring at least 12 years to reach its maturity. To date, there is no reliable molecular marker for identifying sexes before the first bloom, limiting crop designs and utilization. We aimed to identify sex-linked markers for this palm using PCR-based DNA fingerprinting, suppression subtractive hybridization (SSH) and transcriptome sequencing.MethodsDNA fingerprints were generated between males and females based on RAPD, AFLP, SCoT, modified SCoT, ILP, and SSR techniques. Large-scale cloning and screening of SSH libraries and de novo transcriptome sequencing of male and female cDNA from inflorescences were performed to identify sex-specific genes for developing sex-linked markers.ResultsThrough extensive screening and re-testing of the DNA fingerprints (up to 1,204 primer pairs) and transcripts from SSH (>10,000 clones) and transcriptome data, however, no sex-linked marker was identified. Although de novo transcriptome sequencing of male and female inflorescences provided ∼32 million reads and 187,083 assembled transcripts, PCR analysis of selected sex-highly represented transcripts did not yield any sex-linked marker. This result may suggest the complexity and small sex-determining region of the Asian Palmyra palm. To this end, we provide the first global transcripts of male and female inflorescences of Asian Palmyra palm. Interestingly, sequence annotation revealed a large proportion of transcripts related to sucrose metabolism, which corresponds to the sucrose-rich sap produced in the inflorescences, and these transcripts will be useful for further understanding of sucrose production in sugar crop plants. Provided lists of sex-specific and differential-expressed transcripts would be beneficial to the further study of sexual development and sex-linked markers in palms and related species. creator: Kwanjai Pipatchartlearnwong creator: Piyada Juntawong creator: Passorn Wonnapinij creator: Somsak Apisitwanich creator: Supachai Vuttipongchaikij uri: https://doi.org/10.7717/peerj.7268 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Pipatchartlearnwong et al. title: Structure and ion physiology of Brasenia schreberi glandular trichomes in vivo link: https://peerj.com/articles/7288 last-modified: 2019-07-10 description: Brasenia schreberi is a critically endangered aquatic basal angiosperm. In this work, we characterized the structure of the glandular trichomes of B. schreberi morphologically and histochemically. We used a variety of structural, histochemical and permeability stains for the characterization, and we tested the effects of stress in vivo using NaCl and ethanol. We observed that the glandular trichome of B. schreberi are composed of two disk-like stalk cells, and a glandular cell which surround a cuticular storage space. The cuticle is discontinuous at the surface of the shoots. Nearly half of young trichomes senesced in 0.9% NaCl, and mature trichomes senesced at 1.8% NaCl. About half of young trichomes senesced under 3% ethanol and mature trichomes senesced in 2% ethanol after 20 min of treatment. The physiology of glandular trichomes affects the way they secrete mucilage via storage space at a young stage. The trichomes become permeable and absorb ions when mature. This transition depends on the osmiophilic material and the dynamic protoplast. It can accelerate senescence and disassembly by ion accumulation. Permeability tests and ion treatments of glandular trichomes provide new insights for fertilizer research. Our study highlights the structure and physiology of B. schreberi glandular trichomes. creator: Chaodong Yang creator: Xia Zhang creator: Fan Zhang creator: Xiaoe Wang creator: Qingfeng Wang uri: https://doi.org/10.7717/peerj.7288 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Yang et al. title: An attention bias test to assess anxiety states in laying hens link: https://peerj.com/articles/7303 last-modified: 2019-07-10 description: Fear is a response to a known threat, anxiety is a response to a perceived threat. Both of these affective states can be detrimental to animal welfare in modern housing environments. In comparison to the well-validated tests for assessing fear in laying hens, tests for measuring anxiety are less developed. Perception of a threat can result in an attention bias that may indicate anxious affective states in individual hens following playback of an alarm call. In Experiment 1, an attention bias test was applied to hens that differed in their range access to show that hens that never ranged were more vigilant (stretching of the neck and looking around: P < 0.001) and slower to feed following the second alarm call playback (P = 0.01) compared with hens that ranged daily. All hens showed a reduction in comb temperature following the first alarm call (P < 0.001). In Experiment 2, an open field test was used to determine an effective dose of 2 mg/kg for the anxiogenic drug meta-Chlorophenylpiperazine (m-CPP) in adult laying hens. Hens dosed with 2 mg/kg showed reduced locomotion compared with a saline solution (P < 0.05). In Experiment 3, 2 mg/kg m-CPP or saline was administered to adult hens previously habituated to the open field arena to pharmacologically validate an attention bias test as a measure of anxiety. Hens dosed with m-CPP were slower to feed (P = 0.02) and faster to vocalize following a second alarm call playback (P = 0.03) but these hens did not exhibit the same vigilance behavior as documented in Experiment 1. The m-CPP hens also spent more time stepping and vocalizing (both P < 0.001) than the saline hens. An attention bias test could be used to assess anxiety. However, behavioral responses of hens may vary depending on their age or test environment familiarity, thus further refinement of the test is required. In these tests, 2 mg/kg of m-CPP resulted in motionless behavior when the environment was novel, but more movement and vocalizing when the environment was familiar. The extreme behavioral phenotypes exhibited by individually-tested birds may both be indicators of negative states. creator: Dana L.M. Campbell creator: Peta S. Taylor creator: Carlos E. Hernandez creator: Mairi Stewart creator: Sue Belson creator: Caroline Lee uri: https://doi.org/10.7717/peerj.7303 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Campbell et al. title: Bioinformatics analysis of microarray data to identify the candidate biomarkers of lung adenocarcinoma link: https://peerj.com/articles/7313 last-modified: 2019-07-10 description: BackgroundLung adenocarcinoma (LUAD) is the major subtype of lung cancer and the most lethal malignant disease worldwide. However, the molecular mechanisms underlying LUAD are not fully understood.MethodsFour datasets (GSE118370, GSE85841, GSE43458 and GSE32863) were obtained from the gene expression omnibus (GEO). Identification of differentially expressed genes (DEGs) and functional enrichment analysis were performed using the limma and clusterProfiler packages, respectively. A protein–protein interaction (PPI) network was constructed via Search Tool for the Retrieval of Interacting Genes (STRING) database, and the module analysis was performed by Cytoscape. Then, overall survival analysis was performed using the Kaplan–Meier curve, and prognostic candidate biomarkers were further analyzed using the Oncomine database.ResultsTotally, 349 DEGs were identified, including 275 downregulated and 74 upregulated genes which were significantly enriched in the biological process of extracellular structure organization, leukocyte migration and response to peptide. The mainly enriched pathways were complement and coagulation cascades, malaria and prion diseases. By extracting key modules from the PPI network, 11 hub genes were screened out. Survival analysis showed that except VSIG4, other hub genes may be involved in the development of LUAD, in which MYH10, METTL7A, FCER1G and TMOD1 have not been reported previously to correlated with LUAD. Briefly, novel hub genes identified in this study will help to deepen our understanding of the molecular mechanisms of LUAD carcinogenesis and progression, and to discover candidate targets for early detection and treatment of LUAD. creator: Tingting Guo creator: Hongtao Ma creator: Yubai Zhou uri: https://doi.org/10.7717/peerj.7313 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Guo et al. title: Exploring regulatory networks in plants: transcription factors of starch metabolism link: https://peerj.com/articles/6841 last-modified: 2019-07-09 description: Biological networks are complex (non-linear), redundant (cyclic) and compartmentalized at the subcellular level. Rational manipulation of plant metabolism may have failed due to inherent difficulties of a comprehensive understanding of regulatory loops. We first need to identify key factors controlling the regulatory loops of primary metabolism. The paradigms of plant networks are revised in order to highlight the differences between metabolic and transcriptional networks. Comparison between animal and plant transcription factors (TFs) reveal some important differences. Plant transcriptional networks function at a lower hierarchy compared to animal regulatory networks. Plant genomes contain more TFs than animal genomes, but plant proteins are smaller and have less domains as animal proteins which are often multifunctional. We briefly summarize mutant analysis and co-expression results pinpointing some TFs regulating starch enzymes in plants. Detailed information is provided about biochemical reactions, TFs and cis regulatory motifs involved in sucrose-starch metabolism, in both source and sink tissues. Examples about coordinated responses to hormones and environmental cues in different tissues and species are listed. Further advancements require combined data from single-cell transcriptomic and metabolomic approaches. Cell fractionation and subcellular inspection may provide valuable insights. We propose that shuffling of promoter elements might be a promising strategy to improve in the near future starch content, crop yield or food quality. creator: Cristal López-González creator: Sheila Juárez-Colunga creator: Norma Cecilia Morales-Elías creator: Axel Tiessen uri: https://doi.org/10.7717/peerj.6841 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 López-González et al. title: Polyp expansion of passive suspension feeders: a red coral case study link: https://peerj.com/articles/7076 last-modified: 2019-07-09 description: Polyp activity in passive suspension feeders has been considered to be affected by several environmental factors such as hydrodynamics, water temperature and food concentration. To better elucidate the driving forces controlling polyp expansion in these organisms and the potential role of particle concentration, the octocoral Corallium rubrum was investigated in accordance with two approaches: (1) high-frequency in-situ observations examining various environmental and biological variables affecting the water column, and (2) video-recorded flume-controlled laboratory experiments performed under a range of environmental and biological conditions, in terms of water temperature, flow speed, chemical signals and zooplankton. In the field, C. rubrum polyp expansion correlated positively with particle (seston and zooplankton) concentration and current speed. This observation was confirmed by the flume video records of the laboratory experiments, which showed differences in polyp activity due to changes in temperature and current speed, but especially in response to increasing nutritional stimuli. The maximum activity was observed at the highest level of nutritional stimulus consisting of zooplankton. Zooplankton and water movement appeared to be the main factors controlling polyp expansion. These results suggest that the energy budget of passive suspension feeders (and probably the benthic community as a whole) may rely on their ability to maximise prey capture during food pulses. The latter, which may be described as discontinuous organic matter (dead or alive) input, may be the key to a better understanding of benthic-pelagic coupling processes and trophic impacts on animal forests composed of sessile suspension feeders. creator: Sergio Rossi creator: Lucia Rizzo creator: Jean-Claude Duchêne uri: https://doi.org/10.7717/peerj.7076 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Rossi et al. title: A new comprehensive eye-tracking test battery concurrently evaluating the Pupil Labs glasses and the EyeLink 1000 link: https://peerj.com/articles/7086 last-modified: 2019-07-09 description: Eye-tracking experiments rely heavily on good data quality of eye-trackers. Unfortunately, it is often the case that only the spatial accuracy and precision values are available from the manufacturers. These two values alone are not sufficient to serve as a benchmark for an eye-tracker: Eye-tracking quality deteriorates during an experimental session due to head movements, changing illumination or calibration decay. Additionally, different experimental paradigms require the analysis of different types of eye movements; for instance, smooth pursuit movements, blinks or microsaccades, which themselves cannot readily be evaluated by using spatial accuracy or precision alone. To obtain a more comprehensive description of properties, we developed an extensive eye-tracking test battery. In 10 different tasks, we evaluated eye-tracking related measures such as: the decay of accuracy, fixation durations, pupil dilation, smooth pursuit movement, microsaccade classification, blink classification, or the influence of head motion. For some measures, true theoretical values exist. For others, a relative comparison to a reference eye-tracker is needed. Therefore, we collected our gaze data simultaneously from a remote EyeLink 1000 eye-tracker as the reference and compared it with the mobile Pupil Labs glasses. As expected, the average spatial accuracy of 0.57° for the EyeLink 1000 eye-tracker was better than the 0.82° for the Pupil Labs glasses (N = 15). Furthermore, we classified less fixations and shorter saccade durations for the Pupil Labs glasses. Similarly, we found fewer microsaccades using the Pupil Labs glasses. The accuracy over time decayed only slightly for the EyeLink 1000, but strongly for the Pupil Labs glasses. Finally, we observed that the measured pupil diameters differed between eye-trackers on the individual subject level but not on the group level. To conclude, our eye-tracking test battery offers 10 tasks that allow us to benchmark the many parameters of interest in stereotypical eye-tracking situations and addresses a common source of confounds in measurement errors (e.g., yaw and roll head movements). All recorded eye-tracking data (including Pupil Labs’ eye videos), the stimulus code for the test battery, and the modular analysis pipeline are freely available (https://github.com/behinger/etcomp). creator: Benedikt V. Ehinger creator: Katharina Groß creator: Inga Ibs creator: Peter König uri: https://doi.org/10.7717/peerj.7086 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ehinger et al. title: Comparison of olive leaf, olive oil, palm oil, and omega-3 oil in acute kidney injury induced by sepsis in rats link: https://peerj.com/articles/7219 last-modified: 2019-07-09 description: BackgroundHypotension, increased production of reactive oxygen species, and inflammation are all observed in experimental models of sepsis induced by lipopolysaccharide (LPS).PurposeThe aim of this study was to evaluate the effects of an ethanolic extract of Brazilian olive leaf (Ex), Brazilian olive oil (Olv), Ex + Olv (ExOlv), and palm oil (Pal) in comparison to the effects of omega-3 fish oil (Omg) in a rat model of sepsis-induced acute kidney injury.MaterialsWistar rats were divided into seven groups (seven per group), which were either untreated (control) or treated with LPS, LPS + Ex, LPS + ExOlv, LPS + Olv, LPS + Omg, or LPS + Pal.ResultsLower values of creatinine clearance and blood pressure were observed in the LPS-treated group, and these values were not affected by Ex, Olv, ExOlv, Pal, or Omg treatment. Mortality rates were significantly lower in rats exposed to LPS when they were also treated with Ex, ExOlv, Olv, Pal, or Omg. These treatments also decreased oxidative stress and inflammation (Tumor necrosis factor alpha, interleukin-1 beta) and increased interleukin-10 levels and cell proliferation, which were associated with decreased apoptosis in kidney tissue.ConclusionEx and Pal treatments were beneficial in septic rats, since they increased survival rate and did not aggravate inflammation. However, the most effective treatments for septic rats were Olv in comparison to Omg. These natural food substances could enable the development of effective therapeutic interventions to sepsis. creator: Maria Fátima de Paula Ramos creator: Olvania Basso Oliveira creator: Alceni do Carmo Morais Monteiro de Barros creator: Clara Versolato Razvickas creator: Edson de Andrade Pessoa creator: Rinaldo Florêncio da Silva creator: Ana Maria Soares Pereira creator: Marcia Bastos Convento creator: Fernanda Teixeira Borges creator: Nestor Schor uri: https://doi.org/10.7717/peerj.7219 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ramos et al.