title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=384 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Population genetic structure and hybrid zone analyses for species delimitation in the Japanese toad (Bufo japonicus) link: https://peerj.com/articles/16302 last-modified: 2023-10-24 description: Hybridization following secondary contact may produce different outcomes depending on the extent to which genetic diversity and reproductive barriers have accumulated during isolation. The Japanese toad, Bufo japonicus, is distributed on the main islands of Japan. In the present study, we applied multiplexed inter-simple sequence repeat genotyping by sequencing to achieve the fine-scale resolution of the genetic cluster in B. j. japonicus and B. j. formosus. We also elucidated hybridization patterns and gene flow degrees across contact zones between the clusters identified. Using SNP data, we found four genetic clusters in B. j. japonicus and B. j. formosus and three contact zones of the cluster pairs among these four clusters. The two oldest diverged lineages, B. j. japonicus and B. j. formosus, formed a narrow contact zone consistent with species distinctiveness. Therefore, we recommend that these two subspecies be elevated to the species level. In contrast, the less diverged pairs of two clusters in B. j. japonicus and B. j. formosus, respectively, admixed over a hundred kilometers, suggesting that they have not yet developed strong reproductive isolation and need to be treated as conspecifics. These results will contribute to resolving taxonomic confusion in Japanese toads. creator: Kazumi Fukutani creator: Masafumi Matsui creator: Kanto Nishikawa uri: https://doi.org/10.7717/peerj.16302 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Fukutani et al. title: Evaluation of SARS-CoV-2 identification methods through surveillance of companion animals in SARS-CoV-2-positive homes in North Carolina, March to December 2020 link: https://peerj.com/articles/16310 last-modified: 2023-10-24 description: We collected oral and/or rectal swabs and serum from dogs and cats living in homes with SARS-CoV-2-PCR-positive persons for SARS-CoV-2 PCR and serology testing. Pre-COVID-19 serum samples from dogs and cats were used as negative controls, and samples were tested in duplicate at different timepoints. Raw ELISA results scrutinized relative to known negative samples suggested that cut-offs for IgG seropositivity may require adjustment relative to previously proposed values, while proposed cut-offs for IgM require more extensive validation. A small number of pet dogs (2/43, 4.7%) and one cat (1/21, 4.8%) were positive for SARS-CoV-2 RNA, and 28.6 and 37.5% of cats and dogs were positive for anti-SARS-CoV-2 IgG, respectively. creator: Taylor E. Gin creator: Elizabeth A. Petzold creator: Diya M. Uthappa creator: Coralei E. Neighbors creator: Anna R. Borough creator: Craig Gin creator: Erin Lashnits creator: Gregory D. Sempowski creator: Thomas Denny creator: Dorothee Bienzle creator: J. Scott Weese creator: Benjamin J. Callahan creator: Christopher W. Woods uri: https://doi.org/10.7717/peerj.16310 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gin et al. title: ET-1 receptor type B (ETBR) overexpression associated with ICAM-1 downregulation leads to inflammatory attenuation in experimental autoimmune myocarditis link: https://peerj.com/articles/16320 last-modified: 2023-10-24 description: BackgroundAn experimental autoimmune myocarditis rat model was established by subcutaneous injection of porcine myocardial myosin (PCM). The effect of ET-1 receptor type B (ETBR) overexpression on autoimmune myocarditis was observed via tail vein injection of ETBR overexpression lentivirus in rats. We further investigated the mechanisms involved in the regulation of autoimmune myocarditis by ETBR overexpression.MethodsSix rats were randomly selected from 24 male Lewis rats as the NC group, and the remaining 18 rats were injected with PCM on Day 0 and Day 7, to establish the experimental autoimmune myocarditis (EAM) rat model. The 18 rats initially immunized were randomly divided into three groups: the EAM group, ETBR-oe group, and GFP group. On Day 21 after the initial immunization of rats, cardiac echocardiography and serum brain natriuretic peptide (BNP) analysis were performed to evaluate cardiac function, myocardial tissue HE staining was performed to assess myocardial tissue inflammatory infiltration and the myocarditis score, and mRNA expression of IFN-γ, IL-12, and IL-17 was detected by qRT-PCR. Subsequently, immunohistochemical analysis was performed to detect the localization and expression of the ETBR and ICAM-1 proteins, and the expression of ETBR and ICAM-1 was verified by qRT-PCR and western blotting methods.ResultsOn Day 21 after initial immunization, left ventricular end-diastolic diameter (LVEDd), left ventricular end-systolic diameter (LVEDs), and serum BNP concentrations increased in the hearts of rats in the EAM group compared with the NC group (P < 0.01), and ejection fraction (EF) and fractional shortening (FS) decreased compared with those of the normal control (NC) group (P < 0.01). LVEDd, LVEDs, and serum BNP concentrations decreased in the ETBR-oe group compared with the EAM group, while EF and FS increased significantly (P < 0.01). HE staining showed that a large number of inflammatory cell infiltrates, mainly lymphocytes, were observed in the EAM group, and the myocarditis score was significantly higher than that of the NC group (P < 0.01). Compared with that of the EAM group, myocardial tissue inflammatory cell infiltration was significantly reduced in the ETBR-oe group, and the myocarditis scores were significantly lower (P < 0.01). The mRNAs of the inflammatory factors IFN-γ, IL-12 and IL-17 in myocardial tissue of rats in the EAM group exhibited elevated levels compared with those of the NC group (P < 0.01) while the mRNAs of IFN-γ, IL-12 and IL-17 were significantly decreased in the ETBR-oe group compared with the EAM group (P < 0.01). Immunohistochemistry showed that the staining depth of ETBR protein in myocardial tissue was greater in the EAM group than in the NC group, and significantly greater in the ETBR-oe group than in the EAM group, while the staining depth of ICAM-1 was significantly greater in the EAM group than in the NC group, and significantly lower in the ETBR-oe group than in the EAM group. The ICAM-1 expression level was significantly higher in the EAM group than in the NC group (P < 0.01), and was significantly lower in the ETBR-oe groupthan in the EAM group (P < 0.01). creator: Peng Yang creator: Fangfei Li creator: Jiangfeng Tang creator: Qingshan Tian creator: Zhenzhong Zheng uri: https://doi.org/10.7717/peerj.16320 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Yang et al. title: Molecular characterization, expression patterns and cellular localization of BCAS2 gene in male Hezuo pig link: https://peerj.com/articles/16341 last-modified: 2023-10-24 description: BackgroundBreast carcinoma amplified sequence 2 (BCAS2) participates in pre-mRNA splicing and DNA damage response, which is implicated in spermatogenesis and meiosis initiation in mouse. Nevertheless, the physiological roles of BCAS2 in the testes of large mammals especially boars remain largely unknown.MethodsIn this study, testes were collected from Hezuo pig at three development stages including 30 days old (30 d), 120 days old (120 d), and 240 days old (240 d). BCAS2 CDS region was firstly cloned using RT-PCR method, and its molecular characteristics were identified using relevant bioinformatics software. Additionally, the expression patterns and cellular localization of BCAS2 were analyzed by quantitative real-time PCR (qRT-PCR), Western blot, immunohistochemistry and immunofluorescence.ResultsThe cloning and sequence analysis indicated that the Hezuo pig BCAS2 CDS fragment encompassed 678 bp open reading frame (ORF) capable of encoding 225 amino acid residues, and possessed high identities with some other mammals. The results of qRT-PCR and Western blot displayed that BCAS2 levels both mRNA and protein were age-dependent increased (p < 0.01). Additionally, immunohistochemistry and immunofluorescence results revealed that BCAS2 protein was mainly observed in nucleus of gonocytes at 30 d testes as well as nucleus of spermatogonia and Sertoli cells at 120 and 240 d testes. Accordingly, we conclude that BCAS2 is critical for testicular development and spermatogenesis of Hezuo pig, perhaps by regulating proliferation or differentiation of gonocytes, pre-mRNA splicing of spermatogonia and functional maintenance of Sertoli cells, but specific mechanism still requires be further investigated. creator: Yuran Tang creator: Bo Zhang creator: Haixia Shi creator: Zunqiang Yan creator: Pengfei Wang creator: Qiaoli Yang creator: Xiaoyu Huang creator: Shuangbao Gun uri: https://doi.org/10.7717/peerj.16341 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Tang et al. title: Effect of premolar extraction and anchorage type for orthodontic space closure on upper airway dimensions and position of hyoid bone in adults: a retrospective cephalometric assessment link: https://peerj.com/articles/15960 last-modified: 2023-10-23 description: BackgroundThis study aimed to assess the effect of premolar extraction and anchorage type for orthodontic space closure on upper airway dimensions and position of hyoid bone in adults by cephalometric assessment.MethodsThis retrospective study was conducted on 142 cephalograms of patients who underwent orthodontic treatment with premolar extraction in four groups of (I) 40 class I patients with bimaxillary protrusion and maximum anchorage, (II) 40 class I patients with moderate crowding and anchorage, (III) 40 class II patients with maximum anchorage, and (IV) 22 skeletal class III patients with maximum anchorage. The dimensions of the nasopharynx, velopharynx, oropharynx, and hypopharynx, and hyoid bone position were assessed on pre- and postoperative lateral cephalograms using AudaxCeph v6.1.4.3951 software. Data were analyzed by the Chi-square test, paired t-test, and Pearson’s correlation test (alpha = 0.05).ResultsA significant reduction in oropharyngeal, velopharyngeal, and hypopharyngeal airway dimensions was noted in groups I, III, and IV (P < 0.001), which was correlated with the magnitude of retraction of upper and lower incisors (r = 0.6 − 0.8). In group II, a significant increase was observed in oropharyngeal and velopharyngeal dimensions (P < 0.001). A significant increase in nasopharyngeal dimensions occurred in all groups (P < 0.001). Also, in groups I and III, the position of hyoid bone changed downwards and backwards, which was correlated with reduction in airway dimensions (r = 0.4 − 0.6).ConclusionAccording to the present results, extraction orthodontic treatment affects upper airway dimensions and hyoid bone position. Maximum anchorage decreases airway dimensions while moderate anchorage increases airway dimensions. creator: Omid Mortezai creator: Zeynab Shalli creator: Maryam Tofangchiha creator: Ahad Alizadeh creator: Francesco Pagnoni creator: Rodolfo Reda creator: Luca Testarelli uri: https://doi.org/10.7717/peerj.15960 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Mortezai et al. title: No effects of the antiandrogens cyproterone acetate (CPA), flutamide and p,p’-DDE on early sexual differentiation but CPA-induced retardation of embryonic development in the domestic fowl (Gallus gallus domesticus) link: https://peerj.com/articles/16249 last-modified: 2023-10-23 description: Because a wide range of environmental contaminants are known to cause endocrine disorders in humans and animals, in vivo tests are needed to identify such endocrine disrupting chemicals (EDCs) and to assess their biological effects. Despite the lack of a standardized guideline, the avian embryo has been shown to be a promising model system which responds sensitively to EDCs. After previous studies on the effects of estrogenic, antiestrogenic and androgenic substances, the present work focuses on the effects of in ovo exposure to p,p’-DDE, flutamide and cyproterone acetate (CPA) as antiandrogenic model compounds regarding gonadal sex differentiation and embryonic development of the domestic fowl (Gallus gallus domesticus). The substances were injected into the yolk of fertilized eggs on embryonic day one. On embryonic day 19 sex genotype and phenotype were determined, followed by gross morphological and histological examination of the gonads. Treatment with flutamide (0.5, 5, 50 µg/g egg), p,p’-DDE (0.5, 5, 50 µg/g egg) or CPA (0.2, 2, 20 µg/g egg) did not affect male or female gonad development, assessed by gonad surface area and cortex thickness in both sexes and by the percentage of seminiferous tubules in males as endpoints. This leads to the conclusion that antiandrogens do not affect sexual differentiation during embryonic development of G. gallus domesticus, reflecting that gonads are not target organs for androgens in birds. In ovo exposure to 2 and 20 µg CPA/g egg, however, resulted in significantly smaller embryos as displayed by shortened lengths of skull, ulna and tarsometatarsus. Although gonadal endpoints were not affected by antiandrogens, the embryo of G. gallus domesticus is shown to be a suitable test system for the identification of substance-related mortality and developmental delays. creator: Luzie Jessl creator: Jörg Oehlmann uri: https://doi.org/10.7717/peerj.16249 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jessl and Oehlmann title: Parental emotional neglect and academic procrastination: the mediating role of future self-continuity and ego depletion link: https://peerj.com/articles/16274 last-modified: 2023-10-23 description: The purpose of this study was to explore the effect of parental emotional neglect on the academic procrastination of late adolescents and further analyze the mediating role of future self-continuity and ego depletion. This study included 609 college students, 344 males and 265 females, ranging in age from 17 to 21 years (M = 18.39, SD = 0.82), who responded to four questionnaires measuring parental emotional neglect, academic procrastination, future self-continuity, and ego depletion, respectively. The results showed that future self-continuity and ego depletion mediated the association between parental emotional neglect and late adolescents’ academic procrastination in a serial pattern. Perceived higher levels of parental emotional neglect correlated with lower future self-continuity and higher ego depletion in these late adolescents, leading to higher levels of academic procrastination. creator: Chensen Ma creator: Jingjing Song uri: https://doi.org/10.7717/peerj.16274 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ma and Song title: Comprehensive genomic characterisation of the NAC transcription factor family and its response to drought stress in Eucommia ulmoides link: https://peerj.com/articles/16298 last-modified: 2023-10-23 description: The NAC transcription factor family enhances plant adaptation to environmental challenges by participating in signalling pathways triggered by abiotic stressors and hormonal cues. We identified 69 NAC genes in the Eucommia ulmoides genome and renamed them according to their chromosomal distribution. These EuNAC proteins were clustered into 13 sub-families and distributed on 16 chromosomes and 2 scaffolds. The gene structures suggested that the number of exons varied from two to eight among these EuNACs, with a multitude of them containing three exons. Duplicated events resulted in a large gene family; 12 and four pairs of EuNACs were the result of segmental and tandem duplicates, respectively. The drought-stress response pattern of 12 putative EuNACs was observed under drought treatment, revealing that these EuNACs could play crucial roles in mitigating the effects of drought stress responses and serve as promising candidate genes for genetic engineering aimed at enhancing the drought stress tolerance of E. ulmoides. This study provides insight into the evolution, diversity, and characterisation of NAC genes in E. ulmoides and will be helpful for future characterisation of putative EuNACs associated with water deficit. creator: Qi Wang creator: FengCheng Hu creator: ZhaoQun Yao creator: XinFeng Zhao creator: GuangMing Chu creator: Jing Ye uri: https://doi.org/10.7717/peerj.16298 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Machine learning: a powerful tool for identifying key microbial agents associated with specific cancer types link: https://peerj.com/articles/16304 last-modified: 2023-10-23 description: Machine learning (ML) includes a broad class of computer programs that improve with experience and shows unique strengths in performing tasks such as clustering, classification and regression. Over the past decade, microbial communities have been implicated in influencing the onset, progression, metastasis, and therapeutic response of multiple cancers. Host-microbe interaction may be a physiological pathway contributing to cancer development. With the accumulation of a large number of high-throughput data, ML has been successfully applied to the study of human cancer microbiomics in an attempt to reveal the complex mechanism behind cancer. In this review, we begin with a brief overview of the data sources included in cancer microbiomics studies. Then, the characteristics of the ML algorithm are briefly introduced. Secondly, the application progress of ML in cancer microbiomics is also reviewed. Finally, we highlight the challenges and future prospects facing ML in cancer microbiomics. On this basis, we conclude that the development of cancer microbiomics can not be achieved without ML, and that ML can be used to develop tumor-targeting microbial therapies, ultimately contributing to personalized and precision medicine. creator: Jia Feng creator: Kailan Yang creator: Xuexue Liu creator: Min Song creator: Ping Zhan creator: Mi Zhang creator: Jinsong Chen creator: Jinbo Liu uri: https://doi.org/10.7717/peerj.16304 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Feng et al. title: De-novo whole genome assembly of the orange jewelweed, Impatiens capensis Meerb. (Balsaminaceae) using nanopore long-read sequencing link: https://peerj.com/articles/16328 last-modified: 2023-10-23 description: The plant family Balsaminaceae comprises only two genera, and they are a study in contrasts. While Impatiens is an impressively prolific genus, with over 1,000 species and more being discovered each year, its sister genus, Hydrocera, has one solitary species, H. triflora. The two genera also differ in geographic distribution and habitat type (Impatiens species are widely distributed in much of the Old World and N. America, while H. triflora is confined to wetlands specific to S. India, Sri Lanka, and SE Asia). Other contrasting features include plant habit, habitat, floral architecture, mode of seed dispersal, and a host of other traits. The family Balsaminaceae is therefore an excellent model for studying speciation and character evolution as well as understanding the proximal and evolutionary forces that have driven the two genera to adopt such contrasting evolutionary paths. Various species of the Impatiens genus are also commercially important in the ornamental flower industry and as sources of phytochemicals that are of medicinal and other commercial value. As a preliminary step towards studying the genomic basis of the contrasting features of the two genera, we have sequenced and assembled, de novo, the genome of an iconic Impatiens species from N. America, namely I. capensis, and report our findings here. creator: Sudhindra R. Gadagkar creator: J. Antonio Baeza creator: Kristina Buss creator: Nate Johnson uri: https://doi.org/10.7717/peerj.16328 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Gadagkar et al.