title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1302 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Therapeutic effect of Bacillus Calmette–Guerin polysaccharide nucleic acid on mast cell at the transcriptional level link: https://peerj.com/articles/7404 last-modified: 2019-08-21 description: BackgroundChronic spontaneous urticaria (CSU) is a common and recurrent autoimmune-related disease with unclear pathogenesis. Dysfunction of immune cells, such as T cells, mast cells, and basophils, is involved. Bacillus Calmette–Guerin polysaccharide nucleic acid (BCG–PSN), an immunomodulator partially extracted from BCG, can be used in the combined treatment of CSU with an unknown mechanism.MethodsTo study the therapeutic effect and mechanism of BCG–PSN on CSU, we initially assessed the clinical efficacy in 110 enrolled CSU patients of 4-week antihistamine monotherapy vs. antihistamine plus BCG–PSN combined therapy. Subsequently, to explore the further mechanism of BCG-PSN, the mast cell line RBL-2H3 pretreated with BCG-PSN was used to evaluate the transcriptional expression profiles via lncRNA sequencing. Real time PCR was conducted to validate the candidate gene expression.ResultsWe found no significant difference in treatment efficacy between the BCG–PSN group (71.7%) and the monotherapy group (71.9%). However, the average time of complete relief in the BCG–PSN group was significantly shorter than that in the monotherapy group (36.77 ± 17.33 vs. 51.27 ± 16.80, p = 0.026). In vitro experiments showed that BCG-PSN inhibited β-hexosaminidase release rates in IgE-sensitized RBL-2H3 cells (p < 0.001). Sequencing data revealed the expression profiles of functional genes, including a significant decrease in Erb-B2 receptor tyrosine kinase 4, which can be regulated by the nuclear factor kappa B (NF-κB) pathway.DiscussionCSU is a chronic, recurrent disease with complex pathogenesis. Mast cells and basophils are the primary target cells of the disease. BCG–PSN decrease the β-HEX release rates and regulated IgE-mediated mast cell activation in RBL-2H3 cells by mediating immune-related gene expression including ERBB4. These findings suggest that BCG–PSN may mediate ERBB4 expression via the NF-κB pathway and may have value in the treatment of CSU. creator: Siyu Yan creator: Runqiu Liu creator: Manyun Mao creator: Zhaoqian Liu creator: Wei Zhang creator: Yi Zhang creator: Jie Li creator: Cong Peng creator: Xiang Chen uri: https://doi.org/10.7717/peerj.7404 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yan et al. title: Diet and wild ungulate preferences of wolves in northwestern Anatolia during winter link: https://peerj.com/articles/7446 last-modified: 2019-08-21 description: The gray wolf (Canis lupus) is making a comeback in many habitats in central Europe, where it has been once extirpated. Although densities are still low to moderate, this comeback already raises management concerns. In Anatolia, the gray wolf is one of the most common predator species occupying almost all kind of habitats. Although its numbers were reduced in some parts of the country, it has never been extirpated and lived in sympatry with humans. In this study we investigated, for the first time, the winter diet of wolves in north-west Anatolia, where a multispecies wild ungulate community occurs in sympatry with high density livestock. We selected two geographically close but different habitats (steppe and forest) with different wild prey availabilities and compositions. In both areas ungulate contribution to winter diet biomass was more than 90%. Wolf pack size (four to eight wolves) were higher in the study area where livestock numbers and human disturbance were lower and wild prey were more available. In both study areas, wild boar (Sus scrofa) was the main and most preferred food item (Chesson’s α = 0.7 − 0.9) and it occurred at higher density where wolf pack size was smaller. We could not find a high preference (Chesson’s α = 0.3) and high winter predation pressure on the reintroduced Anatolian wild sheep (Ovis gmelinii anatolica) population that occurs in the study area covered by steppe vegetation. Contribution of livestock and food categories other than wild ungulates to wolf diet stayed low. Wolves can help mitigate human-wildlife conflict regulating wild boar numbers, the most common conflict-causing ungulate species in Anatolia. Instead of managing wolf numbers in human dominated landscapes, we recommend reintroduction of wild ungulates to the areas where they became locally extinct and replaced by livestock. creator: Deniz Mengüllüoğlu creator: Eylül İlaslan creator: Hasan Emir creator: Anne Berger uri: https://doi.org/10.7717/peerj.7446 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Mengüllüoğlu et al. title: Phylogenetic analysis of Fritillaria cirrhosa D. Don and its closely related species based on complete chloroplast genomes link: https://peerj.com/articles/7480 last-modified: 2019-08-21 description: Fritillaria cirrhosa D. Don, whose bulb is used in a well-known traditional Chinese medicine to relieve cough and eliminate phlegm, is one of the most important medicinal plants of Fritillaria L. The species is widely distributed among the alpine regions in southwestern China and possesses complex morphological variations in different distributions. A series of newly related species were reported, based on obscure morphological differences. As a result, F. cirrhosa and its closely related species constitute a taxonomically complex group. However, it is difficult to accurately identify these species and reveal their phylogenetic relationships using traditional taxonomy. Molecular markers and gene fragments have been adopted but they are not able to afford sufficient phylogenetic resolution in the genus. Here, we report the complete chloroplast genome sequences of F. cirrhosa and its closely related species using next generation sequencing (NGS) technology. Eight plastid genomes ranged from 151,058 bp to 152,064 bp in length and consisted of 115 genes. Gene content, gene order, GC content, and IR/SC boundary structures were highly similar among these genomes. SSRs and five large repeat sequences were identified and the total number of them ranged from 73 to 79 and 63 to 75, respectively. Six highly divergent regions were successfully identified that could be used as potential genetic markers of Fritillaria. Phylogenetic analyses revealed that eight Fritillaria species were clustered into three clades with strong supports and F. cirrhosa was closely related to F. przewalskii and F. sinica. Overall, this study indicated that the complete chloroplast genome sequence was an efficient tool for identifying species in taxonomically complex groups and exploring their phylogenetic relationships. creator: Qi Chen creator: Xiaobo Wu creator: Dequan Zhang uri: https://doi.org/10.7717/peerj.7480 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Chen et al. title: Genome-wide identification and expression analysis of the VQ gene family in soybean (Glycine max) link: https://peerj.com/articles/7509 last-modified: 2019-08-21 description: BackgroundVQ proteins, the plant-specific transcription factors, are involved in plant development and multiple stresses; however, only few articles systematic reported the VQ genes in soybean.MethodsIn total, we identified 75 GmVQ genes, which were classified into 7 groups (I-VII). Conserved domain analysis indicated that VQ gene family members all contain the VQ domains. VQ genes from the same evolutionary branches of soybean shared similar motifs and structures. Promoter analysis revealed that cis-elements related to stress responses, phytohormone responses and controlling physical as well as reproductive growth. Based on the RNA-seq and qRT-PCR analysis, GmVQ genes were showed expressing in nine tissues, suggesting their putative function in many aspects of plant growth and development as well as response to stress in Glycine max.ResultsThis study aims to understand the roles of VQ genes in various development processes and their expression patterns in responses to stimuli. Our results provide basic information in identification and classification of GmVQ genes. Further experimental analysis will allows us to know the functions of GmVQs participation in plant growth and stress responses. creator: Yongbin Wang creator: Zhenfeng Jiang creator: Zhenxiang Li creator: Yuanling Zhao creator: Weiwei Tan creator: Zhaojun Liu creator: Shaobin Cui creator: Xiaoguang Yu creator: Jun Ma creator: Guangjin Wang creator: Wenbin Li uri: https://doi.org/10.7717/peerj.7509 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Delivery of targeted gene therapies using a hybrid cryogel-coated prosthetic vascular graft link: https://peerj.com/articles/7377 last-modified: 2019-08-20 description: ObjectivesThe success of prosthetic vascular grafts in the management of peripheral arterial disease is frequently limited by the development of anastomotic neointimal hyperplasia (ANIH), with the host response to prosthetic grafts beginning soon after implantation. To address this, we combine a platform of polyethylene terephthalate (PET) fabric with an applied cryogel layer containing biologic agents to create a bioactive prosthetic graft system, with the ability to deliver therapeutics targeting modulators of the ANIH-associated transcriptome response, along with antithrombotic agents.MethodsHybrid graft materials were synthesized by cryopolymerization of methacrylated alginate and heparin onto electrospun (ePET), knitted PET (kPET), or woven PET (wPET). Arg-Gly-Asp (RGD) peptides were added to increase cell adhesion. Scanning electron microscopy (SEM) was used to study the microstructure at 1 day, and 2, 4, and 8 weeks. Physical properties such as swelling ratio, pore connectivity, shape recovery, and stiffness were evaluated. Human aortic endothelial cell (HAoEC) adherence was visualized using confocal microscopy after 24 hours and proliferation was evaluated with a resazurin-based assay for 7 days. Confocal microscopy was used to assess delivery of adeno-associated virus (AAV-GFP) after incubation of hybrid grafts with HAoECs. Heparin activity of the materials was measured using an anti-Xa assay.ResultsSEM demonstrated large interconnected pores throughout the entire structure for all graft types, with minimal degradation of the cryogel after 8 weeks. Hybrid materials showed a trend towards increased shape recovery, increased stiffness, decreased swelling ratio, and no difference in pore connectivity. HAoECs incorporated, adhered, and proliferated over 7 days on all materials. HAoECs were successfully transduced with AAV-GFP from the hybrid graft materials. Anti-Xa assay confirmed continued activity of heparin from all materials for over 7 days.ConclusionsWe have developed a bioactive prosthetic graft system with a cryogel coating capable of delivering biologic agents with antithrombotic activity. By applying the cryogel and selected agents onto PET prior to graft implantation, this study sets the stage for the system to be individualized and tailored to the patient, with bioengineering and targeted gene therapy strategies dovetailing to create an improved prosthetic graft adaptable to emerging knowledge and technologies. creator: Cindy Huynh creator: Ting-Yu Shih creator: Alexander Mammoo creator: Amruta Samant creator: Saif Pathan creator: David W. Nelson creator: Christiane Ferran creator: David Mooney creator: Frank LoGerfo creator: Leena Pradhan-Nabzdyk uri: https://doi.org/10.7717/peerj.7377 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Huynh et al. title: Twisted tale of the tiger: the case of inappropriate data and deficient science link: https://peerj.com/articles/7482 last-modified: 2019-08-20 description: Publications in peer-reviewed journals are often looked upon as tenets on which future scientific thought is built. Published information is not always flawless and errors in published research should be expediently reported, preferably by a peer-review process. We review a recent publication by Gopalaswamy et al. (10.1111/2041-210X.12351) that challenges the use of “double sampling” in large-scale animal surveys. Double sampling is often resorted to as an established economical and practical approach for large-scale surveys since it calibrates abundance indices against absolute abundance, thereby potentially addressing the statistical shortfalls of indices. Empirical data used by Gopalaswamy et al. (10.1111/2041-210X.12351) to test their theoretical model, relate to tiger sign and tiger abundance referred to as an Index-Calibration experiment (IC-Karanth). These data on tiger abundance and signs should be paired in time and space to qualify as a calibration experiment for double sampling, but original data of IC-Karanth show lags of (up to) several years. Further, data points used in the paper do not match the original sources. We show that by use of inappropriate and incorrect data collected through a faulty experimental design, poor parameterization of their theoretical model, and selectively picked estimates from literature on detection probability, the inferences of this paper are highly questionable. We highlight how the results of Gopalaswamy et al. were further distorted in popular media. If left unaddressed, the paper of Gopalaswamy et al. could have serious implications on statistical design of large-scale animal surveys by propagating unreliable inferences. creator: Qamar Qureshi creator: Rajesh Gopal creator: Yadvendradev Jhala uri: https://doi.org/10.7717/peerj.7482 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Qureshi et al. title: Investigating safety profiles of human papillomavirus vaccine across group differences using VAERS data and MedDRA link: https://peerj.com/articles/7490 last-modified: 2019-08-20 description: BackgroundThe safety of vaccines is a critical factor in maintaining public trust in national vaccination programs. This study aimed to evaluate the safety profiles of human papillomavirus (HPV) vaccines with regard to the distribution of adverse events (AE) across gender and age, and the correlations across various AEs using the Food and Drug Administration/Centers for Disease Control and Prevention Vaccine Adverse Event Reporting System (VAERS).MethodsFor analyses, 27,348 patients aged between 9 and 25 years old with at least one AE reported in VAERS between the year of 2006 and 2017 were included. AEs were summarized into two levels: the lower level preferred term (PT) and higher level system organ classes (SOCs) based on the structure of Medical Dictionary for Regulatory Activities (MedDRA). A series of statistical analyses were applied on both levels of AEs. Zero-truncated Poisson regression and multivariate logistic regression models were first developed to assess the rate and risk of SOCs across age groups and genders. Pairwise Pearson correlation analyses and hierarchical clustering analyses were then conducted to explore the interrelationships and clustering pattern among AEs.ResultsWe identified 27,337 unique HPV vaccine reports between 2006 and 2017. Disproportional reporting of AEs was observed across age and gender in 21 SOCs (p < 0.05). The correlation analyses found most SOCs demonstrate weak positive correlations except for five pairs which were negatively correlated: skin and subcutaneous tissue disorders + injury poisoning and procedural complications; skin and subcutaneous tissue disorders + nervous system disorders; Skin and subcutaneous tissue disorders + pregnancy, puerperium and perinatal conditions; nervous system disorders + pregnancy, puerperium and perinatal conditions; pregnancy, puerperium and perinatal conditions + general disorders and administration site conditions. Nervous system disorders had the most AEs which contributed to 12,448 (46%) cases. In the further analyses of correlations between PT in nervous system disorders, the three most strongly correlated AEs were psychiatric disorders (r = 0.35), gastrointestinal disorders (r = 0.215), and musculoskeletal and connective tissue disorders (r = 0.261). We observed an inter-SOCs correlation of the PTs among AE pairs by nervous system disorders/psychiatric disorders/gastrointestinal disorders/musculoskeletal and connective tissue disorders.ConclusionsThe analyses revealed a different distribution pattern of AEs across gender and age subgroups in 21 SOC level AEs. Correlation analyses and hierarchical clustering analyses further revealed several correlated patterns across various AEs. However, findings from this study should be interpreted with caution. Further clinical studies are needed to understand the heterogeneity of AEs reporting across subgroups and the biological pathways among the statistically correlated AEs. creator: Yuxi Jia creator: Cong Zhu creator: Jingcheng Du creator: Yang Xiang creator: Yong Chen creator: Wei Wang creator: Cui Tao uri: https://doi.org/10.7717/peerj.7490 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jia et al. title: Effects of digging by a native and introduced ecosystem engineer on soil physical and chemical properties in temperate grassy woodland link: https://peerj.com/articles/7506 last-modified: 2019-08-20 description: Temperate grasslands and woodlands are the focus of extensive restoration efforts worldwide. Reintroduction of locally extinct soil-foraging and burrowing animals has been suggested as a means to restore soil function in these ecosystems. Yet little is known about the physical and chemical effects of digging on soil over time and how these effects differ between species of digging animal, vegetation types or ecosystems. We compared foraging pits of a native reintroduced marsupial, the eastern bettong (Bettongia gaimardi) and that of the exotic European rabbit (Oryctolagus cuniculus). We simulated pits of these animals and measured pit dimensions and soil chemical properties over a period of 2 years. We showed that bettong and rabbit pits differed in their morphology and longevity, and that pits had a strong moderating effect on soil surface temperatures. Over 75% of the simulated pits were still visible after 2 years, and bettong pits infilled faster than rabbit pits. Bettong pits reduced diurnal temperature range by up to 25 °C compared to the soil surface. We did not find any effects of digging on soil chemistry that were consistent across vegetation types, between bettong and rabbit pits, and with time since digging, which is contrary to studies conducted in arid biomes. Our findings show that animal foraging pits in temperate ecosystems cause physical alteration of the soil surface and microclimatic conditions rather than nutrient changes often observed in arid areas. creator: Catherine E. Ross creator: Nicola T. Munro creator: Philip S. Barton creator: Maldwyn J. Evans creator: John Gillen creator: Ben C.T. Macdonald creator: Sue McIntyre creator: Saul A. Cunningham creator: Adrian D. Manning uri: https://doi.org/10.7717/peerj.7506 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Ross et al. title: Genome-wide identification and characterization of the Hsp70 gene family in allopolyploid rapeseed (Brassica napus L.) compared with its diploid progenitors link: https://peerj.com/articles/7511 last-modified: 2019-08-20 description: Heat shock protein 70 (Hsp70) plays an essential role in plant growth and development, as well as stress response. Rapeseed (Brassica napus L.) originated from recently interspecific hybridization between Brassica rapa and Brassica oleracea. In this study, a total of 47 Hsp70 genes were identified in B. napus (AnAnCnCn genome), including 22 genes from An subgenome and 25 genes from Cn subgenome. Meanwhile, 29 and 20 Hsp70 genes were explored in B. rapa (ArAr genome) and B. oleracea (CoCo genome), respectively. Based on phylogenetic analysis, 114 Hsp70 proteins derived from B. napus, B. rapa, B. oleracea and Arabidopsis thaliana, were divided into 6 subfamilies containing 16 Ar-An and 11 Co-Cn reliable orthologous pairs. The homology and synteny analysis indicated whole genome triplication and segmental duplication may be the major contributor for the expansion of Hsp70 gene family. Intron gain of BnHsp70 genes and domain loss of BnHsp70 proteins also were found in B. napus, associating with intron evolution and module evolution of proteins after allopolyploidization. In addition, transcriptional profiles analyses indicated that expression patterns of most BnHsp70 genes were tissue-specific. Moreover, Hsp70 orthologs exhibited different expression patterns in the same tissue and Cn subgenome biased expression was observed in leaf. These findings contribute to exploration of the evolutionary adaptation of polyploidy and will facilitate further application of BnHsp70 gene functions. creator: Ziwei Liang creator: Mengdi Li creator: Zhengyi Liu creator: Jianbo Wang uri: https://doi.org/10.7717/peerj.7511 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liang et al. title: Movement velocity can be used to estimate the relative load during the bench press and leg press exercises in older women link: https://peerj.com/articles/7533 last-modified: 2019-08-20 description: BackgroundMovement velocity has been proposed as an effective tool to prescribe the load during resistance training in young healthy adults. This study aimed to elucidate whether movement velocity could also be used to estimate the relative load (i.e., % of the one-repetition maximum (1RM)) in older women.MethodsA total of 22 older women (age = 68.2 ± 3.6 years, bench press 1RM = 22.3 ± 4.7 kg, leg press 1RM = 114.6 ± 15.9 kg) performed an incremental loading test during the free-weight bench press and the leg press exercises on two separate sessions. The mean velocity (MV) was collected with a linear position transducer.ResultsA strong linear relationship between MV and the relative load was observed for the bench press (%1RM = −130.4 MV + 119.3; r2 = 0.827, standard error of the estimate (SEE) = 6.10%1RM, p < 0.001) and leg press exercises (%1RM = −158.3 MV + 131.4; r2 = 0.913, SEE = 5.63%1RM, p < 0.001). No significant differences were observed between the bench press and leg press exercises for the MV attained against light-medium relative loads (≤70%1RM), while the MV associated with heavy loads (≥80%1RM) was significantly higher for the leg press.ConclusionsThese results suggest that the monitoring of MV could be useful to prescribe the loads during resistance training in older women. However, it should be noted that the MV associated with a given %1RM is significantly lower in older women compared to young healthy individuals. creator: Pablo Jorge Marcos-Pardo creator: Jorge Miguel González-Hernández creator: Amador García-Ramos creator: Abraham López-Vivancos creator: Pedro Jiménez-Reyes uri: https://doi.org/10.7717/peerj.7533 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Marcos-Pardo et al.