title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=772 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en 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. title: Exploring the potential biomarkers for prognosis of glioblastoma via weighted gene co-expression network analysis link: https://peerj.com/articles/12768 last-modified: 2022-01-18 description: BackgroundGlioblastoma (GBM) is the most common malignant tumor in the central system with a poor prognosis. Due to the complexity of its molecular mechanism, the recurrence rate and mortality rate of GBM patients are still high. Therefore, there is an urgent need to screen GBM biomarkers to prove the therapeutic effect and improve the prognosis.ResultsWe extracted data from GBM patients from the Gene Expression Integration Database (GEO), analyzed differentially expressed genes in GEO and identified key modules by weighted gene co-expression network analysis (WGCNA). GSE145128 data was obtained from the GEO database, and the darkturquoise module was determined to be the most relevant to the GBM prognosis by WGCNA (r =  − 0.62, p = 0.01). We performed enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to reveal the interaction activity in the selected modules. Then Kaplan-Meier survival curve analysis was used to extract genes closely related to GBM prognosis. We used Kaplan-Meier survival curves to analyze the 139 genes in the darkturquoise module, identified four genes (DARS/GDI2/P4HA2/TRUB1) associated with prognostic GBM. Low expression of DARS/GDI2/TRUB1 and high expression of P4HA2 had a poor prognosis. Finally, we used tumor genome map (TCGA) data, verified the characteristics of hub genes through Co-expression analysis, Drug sensitivity analysis, TIMER database analysis and GSVA analysis. We downloaded the data of GBM from the TCGA database, the results of co-expression analysis showed that DARS/GDI2/P4HA2/TRUB1 could regulate the development of GBM by affecting genes such as CDC73/CDC123/B4GALT1/CUL2. Drug sensitivity analysis showed that genes are involved in many classic Cancer-related pathways including TSC/mTOR, RAS/MAPK.TIMER database analysis showed DARS expression is positively correlated with tumor purity (cor = 0.125, p = 1.07e−02)), P4HA2 expression is negatively correlated with tumor purity (cor =−0.279, p = 6.06e−09). Finally, GSVA analysis found that DARS/GDI2/P4HA2/TRUB1 gene sets are closely related to the occurrence of cancer.ConclusionWe used two public databases to identify four valuable biomarkers for GBM prognosis, namely DARS/GDI2/P4HA2/TRUB1, which have potential clinical application value and can be used as prognostic markers for GBM. creator: Mengyuan Zhang creator: Zhike Zhou creator: Zhouyang Liu creator: Fangxi Liu creator: Chuansheng Zhao uri: https://doi.org/10.7717/peerj.12768 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Association between perceived life stress and subjective well-being among Chinese perimenopausal women: a moderated mediation analysis link: https://peerj.com/articles/12787 last-modified: 2022-01-18 description: BackgroundThe impact of perceived life stress on subjective well-being has been well-established; while few studies have explored the mediating and moderating mechanisms of the association between perceived life stress and subjective well-being among perimenopausal women. This study is aimed at exploring the mediating effect of depressive symptoms and the role of interests/hobbies as a moderator in the association between perceived life stress and subjective well-being among perimenopausal women.MethodsThe participants were 1,104 perimenopausal women at the age of 40 to 60, who were asked to complete a paper-based questionnaire. A single item was used to measure self-perceived life stress and interests/hobbies. The Zung Self-rating Depression Scale (SDS) and Subjective Well-being Scale for Chinese Citizens (SWBS-CC) were applied to assess both depressive symptoms and subjective well-being. Multiple linear regression analysis and the PROCESS macro were adopted to analyse not only the mediating effect of depressive symptoms but also the moderating role of interests/hobbies.ResultsPerceived life stress was negatively associated with subjective well-being (B =  − 1.424, β =  − 0.101, P < 0.001). The impact of perceived life stress on subjective well-being was partially mediated by depressive symptoms (mediation effect = −0.760, 95% confidence intervals (CI) [−1.129, −0.415]). In addition, the interaction term between depressive symptoms and interests/hobbies was significantly related to subjective well-being (β =  − 0.060, P < 0.05), indicating moderating effect. Moderated mediation had a significant index (Index = −0.220, SE = 0.099, 95% CI [−0.460, −0.060]).ConclusionsPerceived life stress was negatively related to subjective well-being. The impact of perceived life stress on subjective well-being was mediated by depressive symptoms. Besides, interests/hobbies moderated the indirect effect of depressive symptoms on the relationship between perceived life stress and subjective well-being. creator: Xiangrong Li creator: Zheng Ren creator: Tianliang Ji creator: Hong Shi creator: Hanfang Zhao creator: Minfu He creator: Xinwen Fan creator: Xia Guo creator: Shuang Zha creator: Shuyin Qiao creator: Yuyu Li creator: Yajiao Pu creator: Hongjian Liu creator: Xiumin Zhang uri: https://doi.org/10.7717/peerj.12787 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Li et al. title: A new ancient lineage of ablepharine skinks (Sauria: Scincidae) from eastern Himalayas with notes on origin and systematics of the group link: https://peerj.com/articles/12800 last-modified: 2022-01-18 description: The Himalayas represent a renowned biodiversity hotspot and an important biogeographic realm that has influenced origin and diversification of multiple taxa. A recent herpetological investigation of the eastern Himalayas of the Indian state of Arunachal Pradesh led to the discovery of a unique lineage of ablepharine skink, which is herein described as a new genus along with a new species. The findings are based an integrated taxonomic approach incorporating data from external morphology, microCT scans of the skull and molecular data. The molecular phylogeny of ablepharine skinks is also presented that suggests taxonomic amendments. Discovery of this unique lineage of skinks further highlights the biogeographic importance of the eastern Himalayas as a source for origin of several relic biota. creator: Zeeshan A. Mirza creator: Andrey M. Bragin creator: Harshal Bhosale creator: Gaurang G. Gowande creator: Harshil Patel creator: Nikolay A. Poyarkov uri: https://doi.org/10.7717/peerj.12800 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mirza et al.