title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1306 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Root tolerance and biochemical response of Chinese lettuce (Lactuca sativa L.) genotypes to cadmium stress link: https://peerj.com/articles/7530 last-modified: 2019-08-22 description: This study was conducted to determine the root tolerance and biochemical responses of four Chinese Lactuca sativa L. genotypes (Lüsu, Lümeng, Yidali and Anyan) to cadmium (Cd2+) stress. Twenty-eight days old seedlings were exposed to Hoagland’s nutrient solution supplied with or without 100 µM CdCl2 and monitored for seven days in a climate controlled room. The 100 µM CdCl2 significantly (P < 0.001) decreased all the root morphological indexes of the four genotypes. However, Yidali, which possessed the smallest root system, exhibited greater root tolerance to Cd2+ by having the highest tolerance indexes for root volume (46%), surface area (61%), projected area (74%) and numbers of root forks (63%) and root tips (58%). Moreover, Cd2+ stress also caused increases in H2O2 contents in the roots but the increase was least in Yidali which showed greater root tolerance to Cd2+stress. The effect of Cd2+ stress on the contents of hormones in the roots depended on the genotypes. Under Cd2+ stress, abscisic acid correlated positively with indole-3-acetic acid (r = 0.669*), gibberellic acid (r = 0.630*) and cytokinin (r = 0.785**). The antioxidant enzyme activities and proline responses of the four genotypes to Cd2+ stress were similar. The SOD activity was decreased whiles the CAT and POD activities, as well as the contents of proline increased in all the genotypes under the stress condition. These results suggest that lettuce genotypes with smaller root systems could be more tolerant to Cd2+ stress compared to those with larger root systems. creator: Mohammed Mujitaba Dawuda creator: Weibiao Liao creator: Linli Hu creator: Jihua Yu creator: Jianming Xie creator: Alejandro Calderón-Urrea creator: Xin Jin creator: Yue Wu uri: https://doi.org/10.7717/peerj.7530 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Dawuda et al. title: Development of a multiplex RT-PCR assay for simultaneous detection of Cucumber green mottle mosaic virus and Acidovorax citrulli in watermelon link: https://peerj.com/articles/7539 last-modified: 2019-08-22 description: Watermelon (Citrullus lanatus Thunb.) is considered as a popular and nutritious fruit crop worldwide. Watermelon blood flesh disease caused by Cucumber green mottle mosaic virus (CGMMV) and bacterial fruit blotch caused by Acidovorax citrulli, are two major quarantine diseases of watermelon and result in considerable losses to global watermelon production. In this study, a multiplex reverse-transcription polymerase chain reaction (RT-PCR) method was developed for simultaneous detection of CGMMV and A. citrulli in both watermelon leaves and seeds. Two pairs of specific primers were designed based on the conserved sequences of the genomic RNA of CGMMV and the internal transcribed spacer of A. citrulli, respectively. Transcriptional elongation factor-1α from watermelon was added as an internal reference gene to prevent false negatives. No cross-reactivity was detected with other viral or bacterial pathogens infecting watermelon. Moreover, the multiplex RT-PCR showed high sensitivity and could simultaneously detect CGMMV and A. citrulli as little as 102 copies of plasmid DNA. This method was successfully applied to test field-collected watermelon leaves and stored seeds of cucurbitaceous crops. These results suggested that the developed multiplex RT-PCR technique is a rapid, efficient, and sensitive method for simultaneous detection of CGMMV and A. citrulli, providing technical support for monitoring, predicting, and preventing these two quarantine diseases. To our knowledge, this is the first report on simultaneous detection of a virus and a bacterium by multiplex RT-PCR in watermelon. creator: Xinyue Bi creator: Xiaodong Li creator: Haibo Yu creator: Mengnan An creator: Rui Li creator: Zihao Xia creator: Yuanhua Wu uri: https://doi.org/10.7717/peerj.7539 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Bi et al. title: Perceptual load modulates contour integration in conscious and unconscious states link: https://peerj.com/articles/7550 last-modified: 2019-08-22 description: Previous research has documented that contour detection and integration may either be affected by local features such as the distances between elements or by high-level cognitive factors such as attention in our visual system. Less is known about how low and high level factors interact to influence contour integration. In this paper, we investigated how attention modulates contour integration through saliency (different element spacing) and topological propert ies (circle or S-shaped) when the state of conscious awareness is manipulated. A modified inattentional blindness (IB) combined with the Posner cuing paradigm was adopted in our three-phased experiment (unconscious-training-conscious). Attention was manipulated with high or low perceptual load for a foveal go/no-go task. Cuing effects were utilized to assess the covert processing of contours prior to a peripheral orientation discrimination task. We found that (1) salient circles and S-contours induced different cuing effects under low perceptual load but not with high load; (2) no consistent pattern of cuing effects was found for non-salient contours in all the conditions; (3) a positive cuing effect was observed for salient circles either consciously or unconsciously while a negative cuing effect occurred for salient S-contours only consciously. These results suggest that conscious awareness plays a pivotal role in coordinating a closure effect with the level of perceptual load. Only salient circles can be successfully integrated in an unconscious state under low perceptual load although both salient circles and S-contours can be done consciously. Our findings support a bi-directional mechanism that low-level sensory features interact with high-level cognitive factors in contour integration. creator: Kaiwen Cheng creator: Keyu Yang creator: Long Qin creator: Yixuan Zhuo creator: Hongmei Yan uri: https://doi.org/10.7717/peerj.7550 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cheng et al. title: Middle East Respiratory Syndrome Coronavirus and the One Health concept link: https://peerj.com/articles/7556 last-modified: 2019-08-22 description: Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is one of the major threats to the healthcare systems in some countries, especially in the Arabian Peninsula. MERS-CoV is considered an ideal example of the One Health concept. This is due to the animals, especially dromedary camels, play important roles in the transmission and sustainability of the virus, and the virus can be transmitted through aerosols of infected patients into the environment. However, there is some debate regarding the origin of MERS-CoV either from bats or other unknown reservoirs. The dromedary camel is the only identified animal reservoir to date. These animals play important roles in sustaining the virus in certain communities and may act as an amplifier of the virus by secreting it in their body fluids, especially in nasal and rectal discharges. MERS-CoV has been detected in the nasal and rectal secretions of infected camels, and MERS-CoV of this origin has full capacity to infect human airway epithelium in both in vitro and in vivo models. Other evidence confirms the direct transmission of MERS-CoV from camels to humans, though the role of camel meat and milk products has yet to be well studied. Human-to-human transmission is well documented through contact with an active infected patient or some silently infected persons. Furthermore, there are some significant risk factors of individuals in close contact with a positive MERS-CoV patient, including sleeping in the same patient room, removing patient waste (urine, stool, and sputum), and touching respiratory secretions from the index case. Outbreaks within family clusters have been reported, whereby some blood relative patients were infected through their wives in the same house were not infected. Some predisposing genetic factors favor MERS-CoV infection in some patients, which is worth investigating in the near future. The presence of other comorbidities may be another factor. Overall, there are many unknown/confirmed aspects of the virus/human/animal network. Here, the most recent advances in this context are discussed, and the possible reasons behind the emergence and sustainability of MERS-CoV in certain regions are presented. Identification of the exact mechanism of transmission of MERS-CoV from camels to humans and searching for new reservoir/s are of high priority. This will reduce the shedding of the virus into the environment, and thus the risk of human infection can be mitigated. creator: Maged Gomaa Hemida uri: https://doi.org/10.7717/peerj.7556 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hemida 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.