title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1203 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Monitoring nearshore ecosystem health using Pacific razor clams (Siliqua patula) as an indicator species link: https://peerj.com/articles/8761 last-modified: 2020-03-05 description: An emerging approach to ecosystem monitoring involves the use of physiological biomarker analyses in combination with gene transcription assays. For the first time, we employed these tools to evaluate the Pacific razor clam (Siliqua patula), which is important both economically and ecologically, as a bioindicator species in the northeast Pacific. Our objectives were to (1) develop biomarker and gene transcription assays with which to monitor the health of the Pacific razor clam, (2) acquire baseline biomarker and gene transcription reference ranges for razor clams, (3) assess the relationship between physiological and gene transcription assays and (4) determine if site-level differences were present. Pacific razor clams were collected in July 2015 and 2016 at three sites within each of two national parks in southcentral Alaska. In addition to determining reference ranges, we found differences in biomarker assay and gene transcription results between parks and sites which indicate variation in both large-scale and local environmental conditions. Our intent is to employ these methods to evaluate Pacific razor clams as a bioindicator of nearshore ecosystem health. Links between the results of the biomarker and gene transcription assays were observed that support the applicability of both assays in ecosystem monitoring. However, we recognize the need for controlled studies to examine the range of responses in physiology and gene transcripts to different stressors. creator: Lizabeth Bowen creator: Katrina L. Counihan creator: Brenda Ballachey creator: Heather Coletti creator: Tuula Hollmen creator: Benjamin Pister creator: Tammy L. Wilson uri: https://doi.org/10.7717/peerj.8761 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Bowen et al. title: Recent advances on the estimation of the thermal reaction norm for sex ratios link: https://peerj.com/articles/8451 last-modified: 2020-03-04 description: Temperature-dependent sex determination, or TSD, is a widespread phenomenon in reptiles. The shape of the relationship between constant incubation temperature and sex ratio defines the TSD pattern. The TSD pattern is considered a life-history parameter important for conservation because the wider the range of temperatures producing both sexes, the more resilient the species is to climate change impacts. We review the different published equations and methodologies that have been used to model TSD patterns. We describe a new flexible model that allows for an asymmetrical pattern around the pivotal temperature, which is the constant temperature producing both sexes in equal proportions. We show that Metropolis-Hastings with Markov chain produced by a Monte Carlo process has many advantages compared to maximum likelihood and is preferred. Finally, we apply the models to results from incubation experiments using eggs from the marine turtle Lepidochelys olivacea originating in Northeast Indian, East Pacific, and West Atlantic Regional Management Units (RMUs) and find large differences in pivotal temperatures but not in transitional ranges of temperatures. creator: F. Alberto Abreu-Grobois creator: B. Alejandra Morales-Mérida creator: Catherine E. Hart creator: Jean-Michel Guillon creator: Matthew H. Godfrey creator: Erik Navarro creator: Marc Girondot uri: https://doi.org/10.7717/peerj.8451 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Abreu-Grobois et al. title: Evaluating the repellent effect of four botanicals against two Bactrocera species on mangoes link: https://peerj.com/articles/8537 last-modified: 2020-03-04 description: BackgroundBactrocera dorsalis and B. correcta are economically important fruit fly pests of crops, vegetables, fruits, and nuts worldwide, especially in China. Nowadays in China, B. correcta is a second notorious pest of many fruits after B. dorsalis. Different botanicals have been tested against the B. dorsalis but in the case of B. correcta, no records were published.MethodologyThis study evaluated the repellency of four botanicals (Seriphidium brevifolium, Piper nigrum, Azadirachta indica and quercetin) in acetone dilutions (5%, 2.5% and 1%) against the B. dorsalis and B. correcta at the laboratory conditions (25 ± 2 °C, 60 ± 5% relative humidity, and a photoperiod of L:D 14:10 h).ResultsThe number of visits after 24–48 h, oviposition punctures, and pupae made by both species were lower on the treated mangoes in comparison to untreated mangoes. S. brevifolium, P. nigrum, A. indica and quercetin have significantly reduced the visits, ovipositional punctures, and pupae of both species. Among botanicals, the P. nigrum was the most effective repellent against B. correcta and as well as B. dorsalis. However, the harmful effects of these botanicals against natural enemies are still unknown. creator: Waqar Jaleel creator: Desen Wang creator: Yanyuan Lei creator: Guojun Qi creator: Ting Chen creator: Syed Arif Hussain Rizvi creator: Veeran Sethuraman creator: Yurong He creator: Lihua Lu uri: https://doi.org/10.7717/peerj.8537 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jaleel et al. title: From a calf’s perspective: humpback whale nursing behavior on two US feeding grounds link: https://peerj.com/articles/8538 last-modified: 2020-03-04 description: Nursing influences growth rate and overall health of mammals; however, the behavior is difficult to study in wild cetaceans because it occurs below the surface and can thus be misidentified from surface observations. Nursing has been observed in humpback whales on the breeding and calving grounds, but the behavior remains unstudied on the feeding grounds. We instrumented three dependent calves (four total deployments) with combined video and 3D-accelerometer data loggers (CATS) on two United States feeding grounds to document nursing events. Two associated mothers were also tagged to determine if behavior diagnostic of nursing was evident in the mother’s movement. Animal-borne video was manually analyzed and the average duration of successful nursing events was 23 s (±7 sd, n = 11). Nursing occurred at depths between 4.1–64.4 m (along the seafloor) and in close temporal proximity to foraging events by the mothers, but could not be predicted solely by relative positions of mother and calf. When combining all calf deployments, successful nursing was documented eleven times; totaling only 0.3% of 21.0 hours of video. During nursing events, calves had higher overall dynamic body acceleration (ODBA) and increased fluke-stroke rate (FSR) compared to non-nursing segments (Mixed effect models, ODBA: F1,107 = 13.57756, p = 0.0004, FSR: F1,107 = 32.31018, p < 0.0001). In contrast, mothers had lower ODBA and reduced FSR during nursing events compared to non-nursing segments. These data provide the first characterization of accelerometer data of humpback whale nursing confirmed by animal-borne video tags and the first analysis of nursing events on feeding grounds. This is an important step in understanding the energetic consequences of lactation while foraging. creator: Jennifer E. Tackaberry creator: David E. Cade creator: Jeremy A. Goldbogen creator: David N. Wiley creator: Ari S. Friedlaender creator: Alison K. Stimpert uri: https://doi.org/10.7717/peerj.8538 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tackaberry et al. title: Let’s talk about pain catastrophizing measures: an item content analysis link: https://peerj.com/articles/8643 last-modified: 2020-03-04 description: BackgroundConcerns have been raised about whether self-report measures of pain catastrophizing reflect the construct as defined in the cognitive-behavioral literature. We investigated the content of these self-report measures; that is, whether items assess the construct ‘pain catastrophizing’ and not other theoretical constructs (i.e., related constructs or pain outcomes) using the discriminant content validity method.MethodItems (n = 58) of six pain catastrophizing measures were complemented with items (n = 34) from questionnaires measuring pain-related worrying, vigilance, pain severity, distress, and disability. Via an online survey, 94 participants rated to what extent each item was relevant for assessing pain catastrophizing, defined as “to view or present pain or pain-related problems as considerably worse than they actually are” and other relevant constructs (pain-related worrying, vigilance, pain severity, distress, and disability).ResultsData were analyzed using Bayesian hierarchical models. The results revealed that the items from pain-related worrying, vigilance, pain severity, distress, and disability questionnaires were distinctively related to their respective constructs. This was not observed for the items from the pain catastrophizing questionnaires. The content of the pain catastrophizing measures was equally well, or even better, captured by pain-related worrying or pain-related distress.ConclusionBased upon current findings, a recommendation may be to develop a novel pain catastrophizing questionnaire. However, we argue that pain catastrophizing cannot be assessed by self-report questionnaires. Pain catastrophizing requires contextual information, and expert judgment, which cannot be provided by self-report questionnaires. We argue for a person-centered approach, and propose to rename ‘pain catastrophizing’ measures in line with what is better measured: ‘pain-related worrying’. creator: Geert Crombez creator: Annick L. De Paepe creator: Elke Veirman creator: Christopher Eccleston creator: Gregory Verleysen creator: Dimitri M.L. Van Ryckeghem uri: https://doi.org/10.7717/peerj.8643 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Crombez et al. title: Suppression of osteogenic differentiation and mitochondrial function change in human periodontal ligament stem cells by melatonin at physiological levels link: https://peerj.com/articles/8663 last-modified: 2020-03-04 description: N-Acetyl-5-methoxytryptamine (melatonin, MT) at pharmacological concentrations promotes the osteogenic differentiation of human bone marrow-derived mesenchymal stem cells; however, its role at physiological concentrations (1 pM–10 nM) remains unclear. We explored the effects of 1 pM–1 µM MT on the osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs) and its underlying mitochondrial dynamics-mediated mechanisms. T he PDLSC phenotype was detected by flow cytometry and evaluated for three-line differentiation. Alkaline phosphatase activity assay and Alizarin red staining were used to evaluate osteogenic differentiation. Osteogenesis-related gene and protein expression levels were measured by quantitative reverse transcription -polymerase chain reaction and western blotting. Mitochondrial function assays were performed using reactive oxygen species, ATP and NAD+/NADH kits and molecular mechanisms of mitochondrial dynamics-related proteins were assessed by western blotting. Our results have shown that physiological MT concentrations induced differentiation of hPDLSCs and down-regulated osteopontin (OPN) and osteocalcin (OCN) expression levels, which were restored or even up-regulated by 1 µM MT (lowest pharmacological concentration). Compared to the osteogenic induction alone, this treatment decreased the intracellular ATP content, whereas the intracellular reactive oxygen species level and NAD+/NADH ratio were increased. Mitochondrial function- and dynamics-related protein expression levels were consistent with those of osteogenic genes following osteogenic induction and MT treatment of hPDLSCs at various physiological concentrations. Physiological MT concentrations inhibited the osteogenic differentiation of hPDLSCs and simultaneously altered mitochondrial function. These findings provide insights into the stem cell tissue engineering and functions of MT. creator: Miaomiao Zheng creator: Fuping Zhang creator: Wenguo Fan creator: Liulin Jiang creator: Jingzhou Li creator: Shanshan Xie creator: Fang Huang creator: Hongwen He uri: https://doi.org/10.7717/peerj.8663 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Zheng et al. title: The complete chloroplast genomes of seventeen Aegilops tauschii: genome comparative analysis and phylogenetic inference link: https://peerj.com/articles/8678 last-modified: 2020-03-04 description: The D genome progenitor of bread wheat, Aegilops tauschii Cosson (DD, 2n = 2x = 14), which is naturally distributed in Central Eurasia, ranging from northern Syria and Turkey to western China, is considered a potential genetic resource for improving bread wheat. In this study, the chloroplast (cp) genomes of 17 Ae. tauschii accessions were reconstructed. The cp genome sizes ranged from 135,551 bp to 136,009 bp and contained a typical quadripartite structure of angiosperms. Within these genomes, we identified a total of 124 functional genes, including 82 protein-coding genes, 34 transfer RNA genes and eight ribosomal RNA genes, with 17 duplicated genes in the IRs. Although the comparative analysis revealed that the genomic structure (gene order, gene number and IR/SC boundary regions) is conserved, a few variant loci were detected, predominantly in the non-coding regions (intergenic spacer regions). The phylogenetic relationships determined based on the complete genome sequences were consistent with the hypothesis that Ae. tauschii populations in the Yellow River region of China originated in South Asia not Xinjiang province or Iran, which could contribute to more effective utilization of wild germplasm resources. Furthermore, we confirmed that Ae. tauschii was derived from monophyletic speciation rather than hybrid speciation at the cp genome level. We also identified four variable genomic regions, rpl32-trnL-UAG, ccsA-ndhD, rbcL-psaI and rps18-rpl20, showing high levels of nucleotide polymorphisms, which may accordingly prove useful as cpDNA markers in studying the intraspecific genetic structure and diversity of Ae. tauschii. creator: Qing Su creator: Luxian Liu creator: Mengyu Zhao creator: Cancan Zhang creator: Dale Zhang creator: Youyong Li creator: Suoping Li uri: https://doi.org/10.7717/peerj.8678 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Su et al. title: Fine-mapping of qTGW2, a quantitative trait locus for grain weight in rice (Oryza sativa L.) link: https://peerj.com/articles/8679 last-modified: 2020-03-04 description: BackgroundGrain weight is a grain yield component, which is an integrated index of grain length, width and thickness. They are controlled by a large number of quantitative trait loci (QTLs). Besides major QTLs, minor QTLs play an essential role. In our previous studies, QTL analysis for grain length and width was performed using a recombinant inbred line population derived from rice cross TQ/IRBB lines. Two major QTLs were detected, which were located in proximity to GS3 and GW5 that have been cloned. In the present study, QTLs for grain weight and shape were identified using rice populations that were homozygous at GS3 and GW5.MethodNine populations derived from the indica rice cross TQ/IRBB52 were used. An F10:11population named W1, consisting of 250 families and covering 16 segregating regions, was developed from one residual heterozygote (RH) in the F7generation of Teqing/IRBB52. Three near isogenic line (NIL)-F2 populations, ZH1, ZH2 and ZH3 that comprised 205, 239 and 234 plants, respectively, were derived from three RHs in F10:11. They segregated the target QTL region in an isogenic background. Two NIL populations, HY2 and HY3, were respectively produced from homozygous progeny of the ZH2 and ZH3 populations. Three other NIL-F2 populations, Z1, Z2 and Z3, were established using three RHs having smaller heterozygous segments. QTL analysis for 1000-grain weight (TGW), grain length (GL), grain width (GW), and length/width ratio (LWR) was conducted using QTL IciMapping and SAS procedure with GLM model.ResultA total of 27 QTLs distributed on 12 chromosomes were identified. One QTL cluster, qTGW2/qGL2/qGW2 located in the terminal region of chromosome 2, were selected for further analysis. Two linked QTLs were separated in region Tw31911−RM266. qGL2 was located in Tw31911−Tw32437 and mainly controlled GL and GW. The effects were larger on GL than on GW and the allelic directions were opposite. qTGW2 was located in Tw35293−RM266 and affected TGW, GL and GW with the same allelic direction. Finally, qTGW2 was delimited within a 103-kb region flanked by Tw35293 and Tw35395.ConclusionqTGW2 with significant effects on TGW, GL and GW was validated and fine-mapped using NIL and NIL-F2 populations. These results provide a basis for map-based cloning of qTGW2 and utilization of qTGW2 in the breeding of high-yielding rice varieties. creator: Hui Zhang creator: Yu-Jun Zhu creator: An-Dong Zhu creator: Ye-Yang Fan creator: Ting-Xu Huang creator: Jian-Fu Zhang creator: Hua-An Xie creator: Jie-Yun Zhuang uri: https://doi.org/10.7717/peerj.8679 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhang et al. title: Citrus flavonoids, β-Glucan and organic acid feed additives decrease relative risk during Yersinia ruckeri O1 biotype 2 infection of rainbow trout (Oncorhynchus mykiss) link: https://peerj.com/articles/8706 last-modified: 2020-03-04 description: Whether through direct supplementation of bacteria or by prebiotic supplementation thought to favour subsets of bacteria, modulation of gut microbiota constitutes an important and promising alternative to the use of prophylactic and growth promoting antibiotics in worldwide aquaculture. We fed a commercial base feed, alone or supplemented with either proprietary β-glucan, β-glucan and organic acids, citrus flavonoid or yeast cell wall supplements, to rainbow trout over a period of four weeks. Fish from each feed group were then subjected to experimental, waterborne infection with Yersinia ruckeri O1 biotype 2. Following experimental feeding, the β-glucan and organic acids supplemented group showed significantly improved feed conversion and lipid efficiency ratios. Furthermore, the β-glucan, β-glucan and organic acids and citrus flavonoid supplements proved to significantly reduce the risk of mortality in rainbow trout during experimental infection as shown by hazard ratio analysis. Resulting in 33.2%, 30.6% and 30.5% reduction in risk relative to the non-supplemented base feed, respectively, these three supplements show a promising potential either as stand-alone feed supplements, or as components in complex feed formulations. creator: Kasper Rømer Villumsen creator: Maki Ohtani creator: Torunn Forberg creator: John Tinsley creator: Mette Boye creator: Anders M. Bojesen uri: https://doi.org/10.7717/peerj.8706 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Rømer Villumsen et al. title: Translation, validation and test–retest reliability of the VISA-G patient-reported outcome tool into Danish (VISA-G.DK) link: https://peerj.com/articles/8724 last-modified: 2020-03-04 description: The Victorian Institute of Sport Assessment (VISA) questionnaire model is based on item response theory using a graded response (responses reflect increasing difficulty). The purpose of the VISA-G is to monitor patient outcomes and evaluate treatment strategies for people with greater trochanteric pain syndrome (GTPS). The primary aim of the current study was to translate and culturally adapt the VISA-G into a Danish context (DK) through forward and back translation and cognitive interviews. The second aim was to establish test–retest reliability and face validity of the VISA-G into a Danish context (DK). No major disagreements were observed between the original and translated versions of the questionnaire. A total of 58 heterogenous asymptomatic, and 49 symptomatic respondents (response rate: 92% and 78% respectively) completed the VISA-G.DK twice, 1 week apart. The VISA-G.DK had excellent internal consistency (Cronbach’s alpha: asymptomatic = 0.86; symptomatic = 0.98). The test–retest reliability was excellent for the total score: ICC: 0.961 (95% CI [0.933–0.978]). Standard Error Measurement was calculated to be 0.6. Bland–Altman plots showed no significant or relevant differences from test to retest in the total score with mean differences below 1 (0.61). The minimal detectable change was 3.17 for both groups. The VISA-G.DK was found to be valid, reliable and acceptable for use in the Danish population. creator: Jens Erik Jorgensen creator: Angela M. Fearon creator: Carsten M. Mølgaard creator: Jens Kristinsson creator: Jane Andreasen uri: https://doi.org/10.7717/peerj.8724 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Jorgensen et al.