title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=925 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Ambient ozone pollution at a coal chemical industry city in the border of Loess Plateau and Mu Us Desert: characteristics, sensitivity analysis and control strategies link: https://peerj.com/articles/11322 last-modified: 2021-04-27 description: In this study, ambient ozone (O3) pollution characteristics and sensitivity analysis were carried out in Yulin, a city in the central area of the Loess Plateau during 2017 to 2019 summer. O3 concentrations increased for 2017 to 2019. Correlation and statistics analysis indicated high temperature (T > 25 °C, low relative humidity (RH < 60%), and low wind speed (WS < 3 m/s) were favorable for O3 formation and accumulation, and the O3 pollution days (MDA8 O3 > 160 µg/m3) were predominantly observed when the wind was traveling from the easterly and southerly. O3 concentration in urban area of Yulin was higher than that in background. The pollution air masses from Fenwei Plain increase the level and duration of O3 pollution. In order to clarify the formation mechanism and source of O3, online measurements of volatile organic compounds (VOCs) were conducted from 7 July to 10 August in 2019. The average of VOCs concentration was 26 ± 12 ppbv, and large amounts of alkenes followed by aromatics, characteristic pollutants of the coal chemical industry, were detected in the ambient air. To further measure the sensitivity, the observation-based model (OBM) simulation was conducted. Empirical Kinetic Modeling Approach (EKMA) plot and relative incremental reactivity (RIR) value indicated Yulin located on VOCs-limited regime. That implied a slight decrease of NOx may increase O3 concentration. When the emission reduction ratio of anthropogenic VOCs/NOx higher than 1:1, the O3 will decrease. O3 control strategies analysis shows that the O3 targets of 5% and 10% O3 concentration reductions are achievable through precursor control, but more effort is needed to reach the 30% and 40% reduction control targets. creator: Manfei Yin creator: Xin Zhang creator: Yunfeng Li creator: Kai Fan creator: Hong Li creator: Rui Gao creator: Jinjuan Li uri: https://doi.org/10.7717/peerj.11322 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yin et al. title: Comparative transcriptome analysis reveals key insights into male sterility in Salvia miltiorrhiza Bunge link: https://peerj.com/articles/11326 last-modified: 2021-04-27 description: BackgroundLarge-scale heterosis breeding depends upon stable, inherited male sterility lines. We accidentally discovered a male sterility line (SW-S) in the F1progeny of a Salvia miltiorrhiza Bunge from Shandong, China (purple flowers) crossed with a S. miltiorrhiza f. alba from Sichuan, China (white flowers). We sought to provide insights into the pollen development for male sterility in S. miltiorrhiza.MethodsThe phenotypic and cytological features of the SW-S and fertile control SW-F were observed using scanning electron microscopy and paraffin sections to identify the key stage of male sterility. Transcriptome profiles were recorded for anthers at the tetrad stage of SW-S and SW-F using Illumina RNA-Seq.ResultsThe paraffin sections showed that sterility mainly occurred at the tetrad stage of microspore development, during which the tapetum cells in the anther compartment completely fell off and gradually degraded in the sterile line. There was little-to-no callose deposited around the microspore cells. The tetrad microspore was shriveled and had abnormal morphology. Therefore, anthers at the tetrad stage of SW-S and fertile control SW-F were selected for comparative transcriptome analysis. In total, 266,722,270 clean reads were obtained from SW-S and SW-F, which contained 36,534 genes. There were 2,571 differentially expressed genes (DEGs) in SW-S and SW-F, of which 63.5% were downregulated. Gene Ontology (GO) enrichment analysis indicated that the differentially expressed genes were enriched in 56 functional groups (GO terms); of these, all DEGs involved in microgametogenesis and developmental maturation were downregulated in SW-S. These results were confirmed by quantitative RT-PCR. The two GO terms contained 18 DEGs, among which eight DEGs (namely: GPAT3, RHF1A, phosphatidylinositol, PFAS, MYB96, MYB78, Cals5, and LAT52) were related to gamete development. There were 10 DEGs related to development and maturation, among which three genes were directly related to pollen development (namely: ACT3, RPK2, and DRP1C). Therefore, we believe that these genes are directly or indirectly involved in the pollen abortion of SW-S. Our study provides insight into key genes related to sterility traits in S. miltiorrhiza, and the results can be further exploited in functional and mechanism studies. creator: Yan Yu creator: Yuanyuan Jiang creator: Long Wang creator: Yichao Wu creator: Jinqiu Liao creator: Mingzhi Zhong creator: Ruiwu Yang creator: Xingfu Chen creator: Qingmiao Li creator: Li Zhang uri: https://doi.org/10.7717/peerj.11326 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Yu et al. title: Genome-wide identification, classification, and expression analysis of the HSF gene family in pineapple (Ananas comosus) link: https://peerj.com/articles/11329 last-modified: 2021-04-27 description: Transcription factors (TFs), such as heat shock transcription factors (HSFs), usually play critical regulatory functions in plant development, growth, and response to environmental cues. However, no HSFs have been characterized in pineapple thus far. Here, we identified 22 AcHSF genes from the pineapple genome. Gene structure, motifs, and phylogenetic analysis showed that AcHSF families were distinctly grouped into three subfamilies (12 in Group A, seven in Group B, and four in Group C). The AcHSF promoters contained various cis-elements associated with stress, hormones, and plant development processes, for instance, STRE, WRKY, and ABRE binding sites. The majority of HSFs were expressed in diverse pineapple tissues and developmental stages. The expression of AcHSF-B4b/AcHSF-B4c and AcHSF-A7b/AcHSF-A1c were enriched in the ovules and fruits, respectively. Six genes (AcHSF-A1a , AcHSF-A2, AcHSF-A9a, AcHSF-B1a, AcHSF-B2a, and AcHSF-C1a) were transcriptionally modified by cold, heat, and ABA. Our results provide an overview and lay the foundation for future functional characterization of the pineapple HSF gene family. creator: Lulu Wang creator: Yanhui Liu creator: Mengnan Chai creator: Huihuang Chen creator: Mohammad Aslam creator: Xiaoping Niu creator: Yuan Qin creator: Hanyang Cai uri: https://doi.org/10.7717/peerj.11329 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Wang et al. title: Association between gonadal hormones and osteoporosis in schizophrenia patients undergoing risperidone monotherapy: a cross-sectional study link: https://peerj.com/articles/11332 last-modified: 2021-04-27 description: ObjectivePatients with schizophrenia are at increased risk of osteoporosis. This study first determined the osteoporosis rate in patients with schizophrenia and then then explored the association between serum gonadal hormone levels and osteoporosis among these patients.MethodsA total of 250 patients with schizophrenia and 288 healthy controls were recruited. Osteoporosis was defined by decreased bone mineral density (BMD) of the calcaneus. Serum fasting levels of gonadal hormones (prolactin, estradiol, testosterone, progesterone, follicle-stimulating hormone, luteinizing hormone) were determined. The relationship between osteoporosis and hormone levels was statistically analyzed by binary logistic regression analysis.ResultsOur results showed that patients with schizophrenia had a markedly higher rate of osteoporosis (24.4% vs. 10.1%) than healthy controls (P < 0.001). Patients with osteoporosis were older, had a longer disease course, and had a lower body mass index (BMI) than patients without osteoporosis (all P < 0.05). Regarding gonadal hormones, we found significantly higher prolactin, but lower estradiol, levels in patients with osteoporosis than in those without osteoporosis (both P < 0.05). The regression analysis revealed that PRL (OR = 1.1, 95% CI [1.08–1.15], P < 0.001) and E2 level (OR = 0.9, 95%CI [0.96–0.99], P = 0.011) were significantly associated with osteoporosis in patients with schizophrenia.ConclusionOur results indicate that patients with schizophrenia who are being treated with risperidone have a high rate of osteoporosis. Increased prolactin and reduced estradiol levels are significantly associated with osteoporosis. creator: Yi Chen creator: Yaoyao Zhang creator: Kaili Fan creator: Weiqian Xu creator: Chao Teng creator: Shuangshuang Wang creator: Wei Tang creator: Xiaomin Zhu uri: https://doi.org/10.7717/peerj.11332 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chen et al. title: Identification of potential genes in upper tract urothelial carcinoma using next-generation sequencing with bioinformatics and in vitro analyses link: https://peerj.com/articles/11343 last-modified: 2021-04-27 description: BackgroundWe aimed to identify prognostic biomarkers of upper tract urothelial carcinomas (UTUCs), including microRNAs (miRNAs) and genes which account for only 5% to 10% of all urothelial carcinomas (UCs). In Taiwan, this figure is markedly higher, where it can reach up to 30% of UC cases.Materials and MethodsUsing next-generation sequencing (NGS), we analyzed two pairs of renal pelvis tumors and adjacent normal urothelial tissues to screen miRNAs and messenger RNAs. By combining bioinformatics analysis from miRmap, Gene Expression Omnibus (GEO), and Oncomine and Ingenuity® Pathway Analysis databases, we identified candidate genes. To search for upstream miRNAs with exact target binding sites, we used miRmap, TargetScan, and miRDB to enforce evidence. Then, we clarified gene and protein expression through an in vitro study using western blot analysis and quantitative real-time reverse transcriptase-PCR.ResultsInteractions between selected target genes obtained using the NGS and miRmap methods were assessed through a Venn diagram analysis. Six potential genes, namely, PDE5A, RECK, ZEB2, NCALD, PLCXD3 and CYBRD1 showed significant differences. Further analysis of gene expression from the GEO dataset indicated lower expression of PDE5A, RECK, ZEB2, and CYBRD1 in bladder cancer tissue than in normal bladder mucosa, which indicated that PDE5A, RECK, ZEB2, and CYBRD1 may act as tumor suppressors in UTUC. In addition, we compared the expression of these genes in various UC cell lines (RT4, BFTC905, J82, T24, UMUC3, 5637, BFTC 909, UMUC14) and found decreased expression of PDE5A in muscle-invasive UC cells compared with the RT4 cell line. Furthermore, by using paired UTUC and normal tissues from 20 patients, lower PDE5A expression was also demonstrated in tumor specimens.ConclusionsOur findings suggest these candidate genes may play some roles in UTUC progression. We propose that these markers may be potential targets clarified by in vitro and in vivo experiments. PDE5A also potentially presents tumor suppressor genes, as identified by comparing the expression between normal and tumor specimens. creator: Hsiang-Ying Lee creator: Ching-Chia Li creator: Wei-Ming Li creator: Ya-Ling Hsu creator: Hsin-Chih Yeh creator: Hung-Lung Ke creator: Bi Wen Yeh creator: Chun-Nung Huang creator: Chien-Feng Li creator: Po-Lin Kuo creator: Wen-Jeng Wu uri: https://doi.org/10.7717/peerj.11343 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Lee et al. title: Variation in purple sea urchin (Strongylocentrotus purpuratus) morphological traits in relation to resource availability link: https://peerj.com/articles/11352 last-modified: 2021-04-27 description: Flexible resource investment is a risk sensitive reproductive strategy where individuals trade resources spent on reproduction for basic metabolic maintenance and survival. This study examined morphological variation in herbivorous sea urchin grazers across a mosaic landscape of macroalgae dominated habitats interspersed with patches of sea urchin barrens to determine whether sea urchins shift energy allocation in response to food limitation. Extensive underwater surveys of habitat attributes (e.g., sea urchin density, algae cover) were paired with detailed laboratory assays (e.g., sea urchin dissections) to determine how resource abundance affects energy allocation between reproductive capacity and body structure in the purple sea urchin, Strongylocentrotus purpuratus. We found that: (1) sea urchins had a more elongate jaw structure relative to body size in habitats void of macroalgae (i.e., barrens), (2) sea urchin reproductive capacity (i.e., gonad index) was lower in barrens and the barrens habitat was primarily comprised of encrusting algae, and (3) sea urchin jaw morphology (i.e., lantern index) and reproductive capacity (i.e., gonad index) were inversely related. These results suggest that sea urchins respond to macroalgae limited environments by shifting energy allocation between reproductive capacity and modifications of the foraging apparatus, which may explain the ability of sea urchins to acquire food in resource-limited environments. creator: Joshua G. Smith creator: Sabrina C. Garcia uri: https://doi.org/10.7717/peerj.11352 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Smith and Garcia title: Comparison of morphology, development and expression patterns of hsf and hsp11.0 of Cotesia chilonis under normal and high temperature link: https://peerj.com/articles/11353 last-modified: 2021-04-27 description: Cotesia chilonis (Munakata) is the dominant parasitic wasp of the rice pest, Chilo suppressalis (Walker), and is a valuable parasitic wasp for the prevention and control of C. suppressalis. In this study, developmental indicators and expression of Cchsp11.0 (heat shock protein 11.0) and Cchsf (heat shock factor) were compared for C. chilonis at 27 °C and 36 °C. Developmental duration, morphology, emergence rate, and number of C. chilonis offspring were shortened at 36 °C while the ratio of females to males increased. Cchsp11.0 and Cchsf were highly expressed in the 1st instar stage at 36 °C, and Cchsp11.0 expression gradually decreased as C. chilonis matured; Cchsf expression was not correlated with Cchsp11.0 expression. Compared with 27 °C, the expression pattern of Cchsp11.0 and Cchsf was also not consistent, and Cchsp11.0 expression increased significantly at the adult stage. In conclusion, mildly high temperatures impact growth, development and reproduction of C. chilonis and stimulate the expression of Cchsp11.0 and Cchsf, and Cchsp11.0 and Cchsf play different roles in different developmental stages of C. chilonis at normal and high temperature. creator: Fu-Jing He creator: Feng Zhu creator: Ming-Xing Lu creator: Yu-Zhou Du uri: https://doi.org/10.7717/peerj.11353 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 He et al. title: A Python script to merge Sanger sequences link: https://peerj.com/articles/11354 last-modified: 2021-04-27 description: Merging Sanger sequences is frequently needed during the gene cloning process. In this study, we provide a Python script that is able to assemble multiple overlapping Sanger sequences. The script utilizes the overlapping regions within the tandem Sanger sequences to merge the Sanger sequences. The results demonstrate that the script can produce the merged sequence from the input Sanger sequences in a single run. The script offers a simple and free method for merging Sanger sequences and is useful for gene cloning. creator: Cen Chen creator: Bingguo Lu creator: Xiaofang Huang creator: Chuyun Bi creator: Lili Zhao creator: Yunzhuo Hu creator: Xuanyang Chen creator: Shiqiang Lin creator: Kai Huang uri: https://doi.org/10.7717/peerj.11354 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chen et al. title: A novel one-step quick assay for detection of SARS-COV2 antibodies across mammalian species link: https://peerj.com/articles/11381 last-modified: 2021-04-27 description: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) has so far infected almost a hundred of millions of people and caused more than a million of death across the world. Many serological tests have been developed to track down virus infection in community via identification of antibodies against SARS-CoV2 virus. However, the tests vary in sensitivity, specificity, complexity, and speed. Here, I developed a simple, one-step, quick test to detect antibodies against SARS-CoV2 N (scN) nucleocapsid protein via direct visualization of antigen-antibody reaction. A total of 40 serum samples of SARS-CoV2 patients were purchased from RayBiotech. A total of 50 pre-pandemic human serum samples from San Diego Blood Bank were used as negative controls. After performing the one-step quick test of these 90 serum samples, I found that 39 samples are positive for anti-scN antibodies. All of the 39 positives are from the 40 SARS-CoV2 patients, suggesting that the one-step test is more sensitive than the lateral flow immunoassay (LFIA), the most widely used rapid antibody test. None of the 50 pre-pandemic samples is positive for anti-scN antibodies, indicating that the one-step test has an excellent specificity. The one-step test takes only ~5 min to detect the antibodies; and 1 ml of Escherichia coli culture can produce reagent proteins sufficient for thousands of the tests. Since the one-step test does not need a secondary antibody, it can be used as a universal test for anti-scN antibodies across different mammalian species to track down both human infection and the animal reservoir of SARS-CoV2 virus. creator: Xianjin Zhou uri: https://doi.org/10.7717/peerj.11381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Zhou title: HiCEnterprise: identifying long range chromosomal contacts in Hi-C data link: https://peerj.com/articles/10558 last-modified: 2021-04-26 description: MotivationComputational analysis of chromosomal contact data is currently gaining popularity with the rapid advance in experimental techniques providing access to a growing body of data. An important problem in this area is the identification of long range contacts between distinct chromatin regions. Such loops were shown to exist at different scales, either mediating relatively short range interactions between enhancers and promoters or providing interactions between much larger, distant chromosome domains. A proper statistical analysis as well as availability to a wide research community are crucial in a tool for this task.ResultsWe present HiCEnterprise, a first freely available software tool for identification of long range chromatin contacts not only between small regions, but also between chromosomal domains. It implements four different statistical tests for identification of significant contacts for user defined regions or domains as well as necessary functions for input, output and visualization of chromosome contacts.AvailabilityThe software and the corresponding documentation are available at: github.com/regulomics/HiCEnterprise.Supplementary informationSupplemental data are available in the online version of the article and at the website regulomics.mimuw.edu.pl/wp/hicenterprise. creator: Hanna Kranas creator: Irina Tuszynska creator: Bartek Wilczynski uri: https://doi.org/10.7717/peerj.10558 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Kranas et al.