title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=769 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Biological effects of gamma-ray radiation on tulip (Tulipa gesneriana L.) link: https://peerj.com/articles/12792 last-modified: 2022-01-19 description: Tulip, being an important ornamental plant, generally requires lengthy and laborious procedures to develop new varieties using traditional breeding methods requires. But ionizing radiation potentially accelerates the breeding process of ornamental plant species. The biological effects of γ-ray irradiation on tulip, therefore, were investigated through establishing an irradiation-mediated mutation breeding protocol to accelerate its breeding process. ISSR-PCR molecular marker technique was further used to identify the mutants of phenotypic variation plants. This study showed that low irradiation doses (5 Gy) stimulated bulb germination to improve the survival rate of tulip, while high irradiation doses (20 to 100 Gy) significantly (P < 0.05) inhibited its seed germination and growth, and decreased the flowering rate, petal number, flower stem length and flower diameter. More than 40 Gy significantly (P < 0.05) decreased the total chlorophyll content and increased the malondialdehyde (MDA) content in tulips. Interestingly, three types of both stigma variations and flower pattern variations, and four types of flower colour variations were observed. With increasing the irradiation dose from 5 to 100 Gy, the anthocyanin and flavonoid contents continuously decreased. Scanning electron microscopy (SEM) analysis evidenced that high irradiation doses altered the micromorphology of leaf stomata. Microscopic observations of tulip root apical mitosis further showed the abnormal chromosomal division behaviour occurring at different mitotic phases under irradiation treatment (80 Gy). Increasing the irradiation dose from 20 to 100 Gy enhanced the micronucleus rate. Moreover, the suspected genetic variation in tulips was evaluated by inter-simple sequence repeat (ISSR) analysis, and the percentage of polymorphic bands was 68%. Finally, this study concludes that that 80 Gy may be an appropriate radiation does to better enhance the efficiency of mutagenic breeds in tulip plants. Using γ-ray irradiation, therefore, is expected to offer a theoretical basis for mutation breeding in tulips. creator: Yirui Li creator: Li Chen creator: Xiaodie Zhan creator: Liang Liu creator: Feihong Feng creator: Zihua Guo creator: Dan Wang creator: Hao Chen uri: https://doi.org/10.7717/peerj.12792 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Prokaryotic expression, purification and evaluation of anti-cardiac fibrosis activity of recombinant TGF-β latency associated peptide link: https://peerj.com/articles/12797 last-modified: 2022-01-19 description: BackgroundCardiac fibrosis refers to the abnormal accumulation of extracellular matrix in the heart, which leads to the formation of cardiac scars. It causes systolic and diastolic dysfunction, and ultimately leads to cardiac dysfunction and arrhythmia. TGF-β1 is an important regulatory factor involved in cardiac fibrosis. Studies have shown that the N-terminal latency associated peptide (LAP) must be removed before TGF-β1 is activated. We hypothesize that recombinant LAP may inhibit cardiac fibrosis induced by TGF-β1. To evaluate anti-cardiac fibrosis activity of recombinant LAP, an experimental study was carried out and is reported here.MethodsThe pET28a-LAP plasmid was constructed and transformed into E. coli C43 (DE3) competent cells. The recombinant LAP protein was purified by Ni affinity chromatography. The cells were treated with TGF-β1 at different concentrations for 24 h. The expression of α-SMA was detected by Western blot. RTCA was used to detect the effect of recombinant LAP on the proliferation of H9C2 cells induced by 10 ng/mL TGF-β1. To detect the effect of LAP on the expression of fibrosis-related proteins, H9C2 cells were treated with 10 ng/mL TGF-β1 for 24 h, then added 60 μg/mL recombinant LAP for 48 h. The LAP group was treated with 60 μg/mL recombinant LAP alone. The LAP pre-protection group was treated with 10 ng/mL TGF-β1 and 60 μg/mL recombinant LAP at the same time. Western blot and immunofluorescence were used to detect the expression of α-SMA, collagen I and fibronectin and p-Smad2.ResultsThe recombinant LAP was prokaryotic expressed and purified. 10 ng/mL was determined as the optimal working concentration of TGF-β1 to induce H9C2 cells fibrosis. RTCA results showed that 60 μg/mL LAP could effectively inhibit the proliferation of H9C2 cells induced by TGF-β1. Immunofluorescence results showed that compared with the control group, the fluorescence intensities of α-SMA, collagen I and FN increased significantly after TGF-β1 treatment. The fluorescence intensities in the TGF-β1+LAP group decreased significantly. Western blot results showed that 60 μg/mL LAP could inhibit the increase of α-SMA, collagen I and FN expression in H9C2 cells induced by TGF-β1. Compared with the control, the LAP alone group has no significant difference in α-SMA and p-Smad2 expression level. The expression of α-SMA and p-Smad2 in the TGF-β1 model group was significantly increased compared with the control group. Compared with the TGF-β1 group, both TGF-β1+LAP group and LAP pre-protection group significantly reduced the increase in α-SMA and p-Smad2 levels.ConclusionsRecombinant LAP was prokaryotic expressed and purified. The results showed that recombinant LAP can inhibit the cell proliferation and expression increase of α-SMA, collagen I, fibronectin and p-Smad2 in H9C2 cells induced by TGF-β1. These results suggested that recombinant LAP might inhibit TGF-β1-induced fibrosis of H9C2 cells through the TGF-β/Smad pathway. creator: Xudong Song creator: Yufei Qiu creator: Jiayi Shi creator: Luxin Li creator: Xiaohuan Yuan creator: Dan Wu creator: Yanhui Chu uri: https://doi.org/10.7717/peerj.12797 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Song et al. title: Segmentation of multi-temporal polarimetric SAR data based on mean-shift and spectral graph partitioning link: https://peerj.com/articles/12805 last-modified: 2022-01-19 description: AbstractPolarimetric SAR (PolSAR) image segmentation is a key step in its interpretation. For the targets with time series changes, the single-temporal PolSAR image segmentation algorithm is difficult to provide correct segmentation results for its target recognition, time series analysis and other applications. For this, a new algorithm for multi-temporal PolSAR image segmentation is proposed in this paper. Firstly, the over-segmentation of single-temporal PolSAR images is carried out by the mean-shift algorithm, and the over-segmentation results of single-temporal PolSAR are combined to get the over-segmentation results of multi-temporal PolSAR images. Secondly, the edge detectors are constructed to extract the edge information of single-temporal PolSAR images and fuse them to get the edge fusion results of multi-temporal PolSAR images. Then, the similarity measurement matrix is constructed based on the over-segmentation results and edge fusion results of multi-temporal PolSAR images. Finally, the normalized cut criterion is used to complete the segmentation of multi-temporal PolSAR images. The performance of the proposed algorithm is verified based on three temporal PolSAR images of Radarsat-2, and compared with the segmentation algorithm of single-temporal PolSAR image. Experimental results revealed the following findings: (1) The proposed algorithm effectively realizes the segmentation of multi-temporal PolSAR images, and achieves ideal segmentation results. Moreover, the segmentation details are excellent, and the region consistency is good. The objects which can’t be distinguished by the single-temporal PolSAR image segmentation algorithm can be segmented. (2) The segmentation accuracy of the proposed multi-temporal algorithm is up to 86.5%, which is significantly higher than that of the single-temporal PolSAR image segmentation algorithm. In general, the segmentation result of proposed algorithm is closer to the optimal segmentation. The optimal segmentation of farmland parcel objects to meet the needs of agricultural production is realized. This lays a good foundation for the further interpretation of multi-temporal PolSAR image. creator: Caiqiong Wang creator: Lei Zhao creator: Wangfei Zhang creator: Xiyun Mu creator: Shitao Li uri: https://doi.org/10.7717/peerj.12805 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: High fitness areas drive the aggregation of the sea urchin Mesocentrotus nudus link: https://peerj.com/articles/12820 last-modified: 2022-01-19 description: Sea urchin aggregation is a common phenomenon in coastlines. However, it remains controversial whether sea urchins form resource aggregations or behavioral aggregations in a non-spawning season. To clarify, we studied the aggregative responses to food and predators in the sea urchin Mesocentrotus nudus when high fitness areas (HFAs) were scarce versus sufficient. By taking the occupied area of each sea urchin (test diameter + spines =  4.5 cm) as a square (4.5 cm × 4.5 cm), we set scarce HFAs for the sea urchins in Experiment 1 (the squares of HFAs: the area occupied by experimental sea urchins = 1:1) and sufficient HFAs for the sea urchins in Experiment 2 (the squares of HFAs: the area occupied by experimental sea urchins = 2:1). If M. nudus form resource aggregations, they would aggregate passively under the scarce HFAs conditions, but not in the sufficient HFAs conditions. Conversely, if M. nudus form behavioral aggregation, aggregation would occur in both scarce and sufficient HFAs. The present results showed that in the scarce HFAs, M. nudus in the food and predator groups were significantly closer to the food and further from predators, and had significantly more aggregated numbers in HFAs than those in the control group. Sea urchins did not aggregate in response to food or predators under the sufficient HFAs, although significantly more sea urchins of the experimental group was found in HFAs than that of the control group. Sea urchins (at least M. nudus) form resource aggregations that are driven by the scarce HFAs. This provides valuable information into the mechanisms of the aggregation of sea urchins. creator: Yushi Yu creator: Jiangnan Sun creator: Yaqing Chang creator: Chong Zhao uri: https://doi.org/10.7717/peerj.12820 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yu et al. title: A survey of Cryptosporidium prevalence among birds in two zoos in China link: https://peerj.com/articles/12825 last-modified: 2022-01-19 description: BackgroundCryptosporidiosis is an important zoonotic protozoan disease worldwide, but few studies on this disease have been performed in wild birds; thus, our knowledge of this disease is insufficient, even in zoo birds. Animals in zoos are possible zoonotic disease reservoirs, potentially resulting in zoonotic agent spillover to humans; accordingly, our understanding of such phenomena should be improved.MethodsA total of 263 fresh fecal samples from 43 avian species were randomly collected from the Beijing Zoo and Harbin North Forest Zoo and screened for the prevalence of Cryptosporidium by 18S rRNA gene sequencing. Cryptosporidium species were distinguished based on the combined results of phylogenetic tree and genetic distance analyses conducted with the inclusion of seven avian Cryptosporidium species and 13 avian Cryptosporidium genotypes. The genetic diversity of Cryptosporidium parvum among different hosts, including humans, cattle, dogs, and birds, and the genetic diversity of avian C. parvum among avian hosts in China, Iraq and Brazil were determined based on C. parvum 18S rRNA haplotypes.ResultsThe results of PCR targeting the 18S rRNA gene revealed that 1.9% (5/263) of the samples were Cryptosporidium-positive. Four of the five Cryptosporidium-positive samples originated from white cranes (Grus leucogeranus), and one originated from a flamingo (Phoenicopteridae). Avian C. parvum isolates, including the isolates examined in the present study, showed gene flow with other isolates from different types of hosts, including humans, cattle and dogs, indicating that zoo birds potentially pose zoonotic and pathogenic risks to humans and animals. Additionally, gene flow between avian C. parvum isolates from China and Brazil was detected.ConclusionsTo the best of our knowledge, our results demonstrate C. parvum infection in a flamingo (Phoenicopteridae) and white cranes (Grus leucogeranus) for the first time. The results of our study provide an important reference for understanding the host range, biological characteristics, and molecular epidemiology of C. parvum. creator: Yaxian Lu creator: Tianchun Pu creator: Baohua Ma creator: Lixin Wang creator: Mengchao Zhou creator: Yu Chen creator: Xiuyun Li creator: Changming Zheng creator: Hetong Liu creator: Jinpeng Liu creator: Chunyu Guan creator: Hongyan Yu creator: Chunkuo Dai creator: Yuan Huang creator: Yuling Yang creator: Zhiwei Peng creator: Lei Han creator: Hongliang Chai creator: Zhijun Hou uri: https://doi.org/10.7717/peerj.12825 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lu et al. title: Bioinformatics analysis and identification of hub genes and immune-related molecular mechanisms in chronic myeloid leukemia link: https://peerj.com/articles/12616 last-modified: 2022-01-18 description: BackgroundChronic myeloid leukemia (CML) is a malignant hyperplastic tumor of the bone marrow originating from pluripotent hematopoietic stem cells. The advent of tyrosine kinase inhibitors (TKIs) has greatly improved the survival rate of patients with CML. However, TKI-resistance leads to the disease recurrence and progression. This study aimed to identify immune-related genes (IRGs) associated with CML progression.MethodsWe extracted the gene’s expression profiles from the Gene Expression Omnibus (GEO). Bioinformatics analysis was used to determine the differentially expressed IRGs of CML and normal peripheral blood mononuclear cells (PBMCs). Functional enrichment and gene set enrichment analysis (GSEA) were used to explore its potential mechanism. Hub genes were identified using Molecular Complex Detection (MCODE) and the CytoHubba plugin. The hub genes’ diagnostic value was evaluated using the receiver operating characteristic (ROC). The relative proportions of infiltrating immune cells in each CML sample were evaluated using CIBERSORT. Quantitative real-time PCR (RT-qPCR) was used to validate the hub gene expression in clinical samples.ResultsA total of 31 differentially expressed IRGs were identified. GO analyses revealed that the modules were typically enriched in the receptor ligand activity, cytokine activity, and endopeptidase activity. KEGG enrichment analysis of IRGs revealed that CML involved Th17 cell differentiation, the NF-kappa B signaling pathway, and cytokine-cytokine receptor interaction. A total of 10 hub genes were selected using the PPI network. GSEA showed that these hub genes were related to the gamma-interferon immune response, inflammatory response, and allograft rejection. ROC curve analysis suggested that six hub genes may be potential biomarkers for CML diagnosis. Further analysis indicated that immune cells were associated with the pathogenesis of CML. The RT-qPCR results showed that proteinase 3 (PRTN3), cathepsin G (CTSG), matrix metalloproteinase 9 (MMP9), resistin (RETN), eosinophil derived neurotoxin (RNase2), eosinophil cationic protein (ECP, RNase3) were significantly elevated in CML patients’ PBMCs compared with healthy controls.ConclusionThese results improved our understanding of the functional characteristics and immune-related molecular mechanisms involved in CML progression and provided potential diagnostic biomarkers and therapeutic targets. creator: Fangyi Yao creator: Cui Zhao creator: Fangmin Zhong creator: Tingyu Qin creator: Shuqi Li creator: Jing Liu creator: Bo Huang creator: Xiaozhong Wang uri: https://doi.org/10.7717/peerj.12616 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yao et al. title: Exploring the nitrogen reservoir of biodegradable household garbage and its potential in replacing synthetic nitrogen fertilizers in China link: https://peerj.com/articles/12621 last-modified: 2022-01-18 description: Biodegradable household garbage contains a large amount of nitrogen, which could be used as organic fertilizer to produce organic food and significantly reduce synthetic nitrogen fertilizers. There is limited information on how large the nitrogen reservoir of biodegradable household garbage is in a certain country or region. Here we took China as a case, analyzed the amount of biodegradable household garbage resources and their nitrogen reservoirs. It was noted that the biodegradable household garbage mainly included food waste, waste paper and wood chips, with the amount being 31.56, 29.55, and 6.45 × 106 t·a−1, respectively. Accordingly, the nitrogen reservoirs were 65.31 × 104, 6.80 × 104, and 3.81 × 104 t·a−1 in China. The nitrogen reservoir of food waste accounted for 86% of the total nitrogen reservoir of biodegradable household garbage, which was equivalent to 11% of the amount of actual absorption for synthetic nitrogen fertilizers (6.20 × 106 t·a−1) by agriculture plants in China. Our findings provided a scientific basis for the classification and utilization of biodegradable household garbage. creator: Lan Wang creator: Tianyu Qin creator: Jianshe Zhao creator: Yicheng Zhang creator: Zhiyuan Wu creator: Xiaohui Cui creator: Gaifang Zhou creator: Caihong Li creator: Liyue Guo creator: Gaoming Jiang uri: https://doi.org/10.7717/peerj.12621 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Prediction of active ingredients in Salvia miltiorrhiza Bunge. based on soil elements and artificial neural network link: https://peerj.com/articles/12726 last-modified: 2022-01-18 description: The roots of Salvia miltiorrhiza Bunge. are commonly used in the treatment of cardiovascular diseases, and tanshinones and salvianolic acids are its main active ingredients. However, the composition and content of active ingredients of S. miltiorrhiza planted in different regions of the soil environment are also quite different, which adds new difficulties to the large-scale and standardization of artificial cultivation. Therefore, in this study, we measured the active ingredients in the roots of S. miltiorrhiza and the contents of rhizosphere soil elements from 25 production areas in eight provinces in China, and used the data to develop a prediction model based on BP (back propagation) neural network. The results showed that the active ingredients had different degrees of correlation with soil macronutrients and trace elements, the prediction model had the best performance (MSE = 0.0203, 0.0164; R2 = 0.93, 0.94). The artificial neural network model was shown to be a method that can be used to screen the suitable cultivation sites and proper fertilization. It can also be used to optimize the fertilizer application at specific sites. It also suggested that soil testing formula fertilization should be carried out for medicinal plants like S. miltiorrhiza, which is grown in multiple origins, rather than promoting the use of “special fertilizer” on a large scale. Therefore, the model is helpful for efficient, rational, and scientific guidance of fertilization management in the cultivation of S. miltiorrhiza. creator: Yu Liu creator: Ke Wang creator: Zhu-Yun Yan creator: Xiaofeng Shen creator: Xinjie Yang uri: https://doi.org/10.7717/peerj.12726 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: A review of the common crab genus Macromedaeus Ward, 1942 (Brachyura, Xanthidae) from China Seas with description of a new species using integrative taxonomy methods link: https://peerj.com/articles/12735 last-modified: 2022-01-18 description: Macromedaeus is one of the most common xanthid genera in shallow waters of the Indo-West Pacific. In this study, we describe a new species, Macromedaeus hainanensis sp. nov., and report on two newly recorded species, M. quinquedentatus (Krauss, 1843) and M. orientalis (Takeda & Miyake, 1969) from Hainan Island, South China Sea. M. hainanensis is most related to M. distinguendus (De Haan, 1833-1850) and M. orientalis on the carapace shape and granular appearance, but can be distinguished by unique morphological characteristics especially its front, pereopods and male first gonopod. Taxonomic identities of the six Macromedaeus species recorded from China seas are discussed, and a phylogenetic analyzation is performed on Macromedaeus and related taxa based on three mitochondrial and two nuclear markers (12S, 16S, COI, H3, 18S). Integrated taxonomic evidence is used to support the taxonomic status of each species. creator: Ziming Yuan creator: Wei Jiang creator: Zhongli Sha uri: https://doi.org/10.7717/peerj.12735 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Yuan et al. title: Genome survey sequencing of the phyto-parasitic nematode Hoplolaimus galeatus link: https://peerj.com/articles/12749 last-modified: 2022-01-18 description: BackgroundHoplolaimus galeatus is a plant-parasite nematode with a broad range of hosts. This nematode is known to damage cotton, corn, and soybean crops. Hoplolaimus galeatus is also an economically important pest of turfgrasses. Despite its economical importance, no genomic resources exist for this parasite.MethodsUsing 300 bp paired-end short read sequencing, this study estimated genome size, analyzed a nearly complete mitochondrial chromosome, and explored nuclear repetitive elements, including microsatellites, in H. galeatus for the first time. The phylogenetic placement of H. galeatus in the superfamily Tylenchoidea was also examined.ResultsThe average haploid genome size estimated using a k-mer approach was 517.69 Mbp. The partially assembled mitochondrial genome of H. galeatus is 16,578 bp in length and comprised of 11 protein-coding genes, two ribosomal RNA genes, and 16 transfer RNA genes. A maximum likelihood phylogenetic analysis confirmed the monophyly of the genus Hoplolaimus and the superfamily Tylenchoidea. Repetitive elements constituted  50% of the nuclear genome while half of the genome represented single- or low-copy sequences. A large portion of repetitive sequences could not be assigned to known repeat element families. Considering only annotated repetitive elements, the most ubiquitous belonged to Class II- Subclass 2-Maverick elements, Class I-LTR-Ty-3/Bel-Pao elements, and satellites. 45S ribosomal DNA was also abundant and a total of 36 SSRs were identified.This study developed genomic resources for the plant-parasitic nematode Hoplolaimus galeatus that will contribute to the better understanding of meta-population connectivity and putative genomic mechanisms involved in the exploitation of the broad range of host plants used by H. galeatus. creator: Xinyuan Ma creator: Paula Agudelo creator: Vincent P. Richards creator: J. Antonio Baeza uri: https://doi.org/10.7717/peerj.12749 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ma et al.