title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1101 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: A novel histozoic myxosporean, Enteromyxum caesio n. sp., infecting the redbelly yellowtail fusilier, Caesio cuning, with the creation of the Enteromyxidae n. fam., to formally accommodate this commercially important genus link: https://peerj.com/articles/9529 last-modified: 2020-07-14 description: Gastrointestinal myxosporean parasites from the genus Enteromyxum are known to cause severe disease, resulting in high mortalities in numerous species of cultured marine fishes globally. Originally described as Myxidium spp., they were transferred to a new genus, Enteromyxum, to emphasize their novel characteristics. Their retention in the family Myxidiidae at the time was warranted, but more comprehensive phylogenetic analyses have since demonstrated the need for a new family for these parasites. We discovered a novel Enteromyxum in wild fish from Malaysia and herein describe the fourth species in the genus and erect a new family, the Enteromyxidae n. fam., to accommodate them. Enteromyxum caesio n. sp. is described infecting the tissues of the stomach in the redbelly yellowtail fusilier, Caesio cuning, from Malaysia. The new species is distinct from all others in the genus, as the myxospores although morphologically similar, are significantly smaller in size. Furthermore, small subunit ribosomal DNA sequence data reveal that E. caesio is <84% similar to others in the genus, but collectively they form a robust and discrete clade, the Enteromyxidae n. fam., which is placed as a sister taxon to other histozoic marine myxosporeans. In addition, we describe, using transmission electron microscopy, the epicellular stages of Enteromyxum fugu and show a scanning electron micrograph of a mature myxospore of E. caesio detailing the otherwise indistinct sutural line, features of the polar capsules and spore valve ridges. The Enteromyxidae n. fam. is a commercially important group of parasites infecting the gastrointestinal tract of marine fishes and the histozoic species can cause the disease enteromyxosis in intensive finfish aquaculture facilities. Epicellular and sloughed histozoic stages are responsible for fish-to-fish transmission in net pen aquaculture systems but actinospores from an annelid host are thought to be necessary for transmission to fish in the wild. creator: Mark A. Freeman creator: Tetsuya Yanagida creator: Àrni Kristmundsson uri: https://doi.org/10.7717/peerj.9529 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Freeman et al. title: Soil macro-fauna respond to environmental variations along a coastal-inland gradient link: https://peerj.com/articles/9532 last-modified: 2020-07-14 description: Varied environmental conditions in coastal-inland zones tend to influence soil faunal communities. However, few studies have focused on the responses of soil fauna to environmental variations along the coastal-inland gradient. In order to better understand the aforementioned responses, a total of 80 soil macro-faunal samples were collected at the five different distances from the coastline of China’s Bohai Bay. The results revealed that the compositions, structural characteristics and diversity of the soil macro-fauna varied among the different habitats. With the increases in the distance from the sea, the individual density, richness and diversity levels of the soil macro-fauna all first increased and then decreased. The individual density, richness and diversity values were all at their maximum at 30 km from the sea. The Edge effect promoted unique and rare soil macro-faunal taxa. Formicidae, Curculionidae and Aphodiidae were found to be the edge taxa. Agelenidae, Liocranidae and Nematocera were considered to be indicator taxa of severe sea effects. Paradoxosomatidae was an indicator taxon of slight effects. Overall, the environmental variations along the coastal-inland gradient were found to have the potential to affect the soil macro-faunal communities, and the different taxa of the soil macro-fauna responded to those variations in different ways. This study further revealed the processes and mechanisms of the sea influencing the soil macro-faunal communities, which had been caused by the coastal-inland gradient. The results of this study also provided a theoretical basis for developing future biodiversity guidelines for coastal ecosystems. creator: Xiaoxue Zheng creator: Yan Tao creator: Zhongqiang Wang creator: Chen Ma creator: Hong He creator: Xiuqin Yin uri: https://doi.org/10.7717/peerj.9532 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zheng et al. title: Predictive values of stool-based tests for mucosal healing among Taiwanese patients with ulcerative colitis: a retrospective cohort analysis link: https://peerj.com/articles/9537 last-modified: 2020-07-14 description: Background/PurposeOver the past two decades, ulcerative colitis (UC) has emerged in the Asia Pacific area, and its treatment goal has shifted from symptom relief to endoscopic remission. Endoscopy is the gold standard for the assessment of mucosal healing; however, it is an invasive method. Fecal calprotectin (FC) is a non-invasive stool-based inflammatory marker which has been used to monitor mucosal healing status, but it is expensive. By contrast, the immune fecal occult blood test (iFOBT) is a widely utilized stool-based screening tool for colorectal cancer. In this study, we compared the predictive values of iFOBT and FC for mucosal healing in Taiwanese patients with UC.MethodsA total of 50 patients with UC identified via the electronic clinical database of Changhua Christian Hospital, Taiwan, were retrospectively enrolled from January 2018 to July 2019. Results of iFOBT, FC level, and blood tests as well as Mayo scores were reviewed and analyzed. Colonic mucosa was evaluated using the endoscopic Mayo subscore.ResultsThe average age of the patients was 46 years, and 62% of the patients were men. Disease distribution was as follows: E1 (26%), E2 (40%), and E3 (34%). Complete mucosal healing (Mayo score = 0) was observed in 30% of patients. Endoscopic mucosal healing with a Mayo score of 0 or 1 was observed in 62% of the patients. Results of FC and iFOBT were compared among patients with and without mucosal healing. Predictive cutoff values were analyzed using receiver operating characteristics curves. iFOBT and FC had similar area under the curve for both complete mucosal healing (0.813 vs. 0.769, respectively, p = 0.5581) and endoscopic mucosal healing (0.906 vs. 0.812, respectively, p = 0.1207).ConclusionIn daily clinical practice, FC and iFOBT do not differ in terms of predictive values for mucosal healing among Taiwanese patients with UC. creator: Hsu-Heng Yen creator: Mei-Wen Chen creator: Yu-Yao Chang creator: Hsuan-Yuan Huang creator: Tsui-Chun Hsu creator: Yang-Yuan Chen uri: https://doi.org/10.7717/peerj.9537 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Yen et al. title: Bioinformatics analysis and identification of circular RNAs promoting the osteogenic differentiation of human bone marrow mesenchymal stem cells on titanium treated by surface mechanical attrition link: https://peerj.com/articles/9292 last-modified: 2020-07-13 description: BackgroundTo analyze and identify the circular RNAs (circRNAs) involved in promoting the osteogenic differentiation of human bone mesenchymal stem cells (hBMSCs) on titanium by surface mechanical attrition treatment (SMAT).MethodsThe experimental material was SMAT titanium and the control material was annealed titanium. Cell Counting Kits-8 (CCK-8) was used to detect the proliferation of hBMSCs, and alkaline phosphatase (ALP) activity and alizarin red staining were used to detect the osteogenic differentiation of hBMSCs on the sample surfaces. The bioinformatics prediction software miwalk3.0 was used to construct competing endogenous RNA (ceRNA) networks by predicting circRNAs with osteogenesis-related messenger RNAs (mRNAs) and microRNAs (miRNAs). The circRNAs located at the key positions in the networks were selected and analyzed by quantitative real-time PCR (QRT-PCR).ResultsCompared with annealed titanium, SMAT titanium could promote the proliferation and osteogenic differentiation of hBMSCs. The total number of predicted circRNAs was 51. Among these, 30 circRNAs and 8 miRNAs constituted 6 ceRNA networks. Circ-LTBP2 was selected for verification. QRT-PCR results showed that the expression levels of hsa_circ_0032599, hsa_circ_0032600 and hsa_circ_0032601 were upregulated in the experimental group compared with those in the control group; the differential expression of hsa_circ_0032600 was the most obvious and statistically significant, with a fold change (FC) = 4.25 ± 1.60, p-values (p) < 0.05. creator: Shanshan Zhu creator: Yuhe Zhu creator: Zhenbo Wang creator: Chen Liang creator: Nanjue Cao creator: Ming Yan creator: Fei Gao creator: Jie Liu creator: Wei Wang uri: https://doi.org/10.7717/peerj.9292 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhu et al. title: High frequency direct shoot regeneration from Kazakh commercial potato cultivars link: https://peerj.com/articles/9447 last-modified: 2020-07-13 description: Potato (Solanum tuberosum L.) is the third most economically important crop in the world and has a high nutritional value. In this study, the in vitro culture response of four widely grown in Kazakhstan potato cultivars, Astanalyk, Monument Kunaev, Tokhtar, and Aksor, was investigated using stem and leaf explants. Published protocols were evaluated and optimized to develop a more efficient protocol for the regeneration of plants from local potato cultivars in tissue culture, which is a prerequisite to facilitate potato genome modification. The explants were cultured on solid Murashige and Skoog medium supplemented with different concentrations and combinations of zeatin, 6-benzylaminopurine (BAP), gibberellic acid (GA3), 1-naphthaleneacetic acid (NAA) and indole-3-acetic acid (IAA). The maximum regeneration was induced from the stem internodal explants. A significant effect of the explant source on direct regeneration was confirmed with statistical analysis. The number of shoots obtained from the internode was 10.0 from cv. Aksor followed by cvs. Tokhtar and Astanalyk. The medium DRM-VIII with 1 mg/l zeatin, 0.1 mg/l IAA and 7.0 mg/l GA3 was considered the best for direct shoot regeneration and multiple shoot formation from all cultivars. To conclude, we outline a protocol for direct plant regeneration from four potato cultivars. Our findings suggest commercial cultivars Astanalyk and Aksor are good candidates for developing the genome-edited plants through direct shoot regeneration. creator: Laura S. Abeuova creator: Balnur R. Kali creator: Aizhan O. Rakhimzhanova creator: Sara S. Bekkuzhina creator: Shuga A. Manabayeva uri: https://doi.org/10.7717/peerj.9447 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Abeuova et al. title: Plastome comparative genomics in maples resolves the infrageneric backbone relationships link: https://peerj.com/articles/9483 last-modified: 2020-07-13 description: Maples (Acer) are among the most diverse and ecologically important tree genera of the north-temperate forests. They include species highly valued as ornamentals and as a source of timber and sugar products. Previous phylogenetic studies employing plastid markers have not provided sufficient resolution, particularly at deeper nodes, leaving the backbone of the maple plastid tree essentially unresolved. We provide the plastid genome sequences of 16 species of maples spanning the sectional diversity of the genus and explore the utility of these sequences as a source of information for genetic and phylogenetic studies in this group. We analyzed the distribution of different types of repeated sequences and the pattern of codon usage, and identified variable regions across the plastome. Maximum likelihood and Bayesian analyses using two partitioning strategies were performed with these and previously published sequences. The plastomes ranged in size from 155,212 to 157,023 bp and had structure and gene content except for Acer palmatum (sect. Palmata), which had longer inverted repeats and an additional copy of the rps19 gene. Two genes, rps2 and rpl22, were found to be truncated at different positions and might be non-functional in several species. Most dispersed repeats, SSRs, and overall variation were detected in the non-coding sequences of the LSC and SSC regions. Fifteen loci, most of which have not been used before in the genus, were identified as the most variable and potentially useful as molecular markers for barcoding and genetic studies. Both ML and Bayesian analyses produced similar results irrespective of the partitioning strategy used. The plastome-based tree largely supported the topology inferred in previous studies using cp markers while providing resolution to the backbone relationships but was highly incongruous with a recently published nuclear tree presenting an opportunity for further research to investigate the causes of discordance, and particularly the role of hybridization in the diversification of the genus. Plastome sequences are valuable tools to resolve deep-level relationships within Acer. The variable loci and SSRs identified in this study will facilitate the development of markers for ecological and evolutionary studies in the genus. This study underscores the potential of plastid genome sequences to improve our understanding of the evolution of maples. creator: Fabiola Areces-Berazain creator: Yixi Wang creator: Damien D. Hinsinger creator: Joeri S. Strijk uri: https://doi.org/10.7717/peerj.9483 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Areces-Berazain et al. title: Evolutionary history of a Scottish harbour seal population link: https://peerj.com/articles/9167 last-modified: 2020-07-10 description: Efforts to conserve marine mammals are often constrained by uncertainty over their population history. Here, we examine the evolutionary history of a harbour seal (Phoca vitulina) population in the Moray Firth, northeast Scotland using genetic tools and microsatellite markers to explore population change. Previous fine-scale analysis of UK harbour seal populations revealed three clusters in the UK, with a northeastern cluster that included our Moray Firth study population. Our analysis revealed that the Moray Firth cluster is an independent genetic group, with similar levels of genetic diversity across each of the localities sampled. These samples were used to assess historic abundance and demographic events in the Moray Firth population. Estimates of current genetic diversity and effective population size were low, but the results indicated that this population has remained at broadly similar levels following the population bottleneck that occurred after post-glacial recolonization of the area. creator: Natacha Nikolic creator: Paul Thompson creator: Mark de Bruyn creator: Matthias Macé creator: Claude Chevalet uri: https://doi.org/10.7717/peerj.9167 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nikolic et al. title: First report of begomoviruses infecting Cucumis sativus L. in North America and identification of a proposed new begomovirus species link: https://peerj.com/articles/9245 last-modified: 2020-07-10 description: BackgroundMembers of the Begomovirus genus are phytopathogens that infect dicotyledonous plants, producing economic losses in tropical and subtropical regions. To date, only seven species of begomoviruses (BGVs) infecting cucumber have been described. Most cucumber infections were reported in South Asia. In the Americas, begomoviral infections affecting cucumber are scarce; just one report of begomovirus has been described in South America. The presence of whitefly and typical symptoms of viral infections observed in a cucumber field in Colima, Mexico, suggested that plants in this field were affected by BGVs.MethodsTo identify the BGVs infecting cucumber, we performed a high-throughput sequencing and compared the assembled contigs against the GenBank nucleic acid sequence database. To confirm the presence of viruses in cucumber samples, we performed a PCR detection using specific oligonucleotides. We cloned and sequenced by Sanger method the complete genome of a potential new begomovirus. Begomovirus species demarcation was performed according to the International Committee on Taxonomy of Viruses. The evolutionary relationship of the new virus was inferred using phylogenetic and recombination analyses.ResultsWe identified five species of begomovirus infecting plants in a field. None of these have been previously reported infecting cucumber. One of the five species of viruses here reported is a new begomovirus species. Cucumber chlorotic leaf virus, the new species, is a bipartite begomovirus that has distinctive features of viruses belonging to the squash leaf curl virus clade.ConclusionsThe findings here described represent the first report of begomoviral infection affecting cucumber plants in North America. Previous to this report, only seven begomovirus species have been reported in the world, here we found five species infecting cucumber plants in a small sample suggesting that cucumber is vulnerable to BGVs. One of these viruses is a new species of begomovirus which is the first begomovirus originally isolated from the cucumber. The findings of this report could help to develop strategies to fight the begomoviral infections that affect cucumber crops. creator: Sarahi Sanchez-Chavez creator: Carlos Fernando Regla-Marquez creator: Zugey Elizabeth Cardenas-Conejo creator: Daniel Alejandro Garcia-Rodriguez creator: Sara Centeno-Leija creator: Hugo Serrano-Posada creator: Andromeda Liñan-Rico creator: Brenda Lizet Partida-Palacios creator: Yair Cardenas-Conejo uri: https://doi.org/10.7717/peerj.9245 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sanchez-Chavez et al. title: Analysis of conserved miRNAs in cynomolgus macaque genome using small RNA sequencing and homology searching link: https://peerj.com/articles/9347 last-modified: 2020-07-10 description: MicroRNAs (miRNAs) are important regulators that fine-tune diverse cellular activities. Cynomolgus macaques (Macaca fascicularis) are used extensively in biomedical and pharmaceutical research; however, substantially fewer miRNAs have been identified in this species than in humans. Consequently, we investigated conserved miRNA profiles in cynomolgus macaques by homology searching and small RNA sequencing. In total, 1,455 high-confidence miRNA gene loci were identified, 408 of which were also confirmed by RNA sequencing, including 73 new miRNA loci reported in cynomolgus macaques for the first time. Comparing miRNA expression with age, we found a positive correlation between sequence conservation and expression levels during miRNA evolution. Additionally, we found that the miRNA gene locations in cynomolgus macaque genome were very flexible. Most were embedded in intergenic spaces or introns and clustered together. Several miRNAs were found in certain gene locations, including 64 exon-resident miRNAs, six splice-site-overlapping miRNAs (SO-miRNAs), and two pairs of distinct mirror miRNAs. We also identified 78 miRNA clusters, 68 of which were conserved in the human genome, including 10 large miRNA clusters predicted to regulate diverse developmental and cellular processes in cynomolgus macaque. Thus, this study not only expands the number of identified miRNAs in cynomolgus macaques but also provides clues for future research on the differences in miRNA repertoire between macaques and humans. creator: Xia Huang creator: Shijia Li creator: Xiaoming Liu creator: Shuting Huang creator: Shuang Li creator: Min Zhuo uri: https://doi.org/10.7717/peerj.9347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Huang et al. title: Analysis of factors contributing to postoperative body weight change in patients with gastric cancer: based on generalized estimation equation link: https://peerj.com/articles/9390 last-modified: 2020-07-10 description: AimsThe study aimed to explore factors contributing to body weight change over time in gastric cancer patients after gastrectomy, in order to find risk factors to implement nutritional intervention beforehand.MethodsA cohort of gastric cancer patients who were treated with gastrectomy from January to March 2019 at a university affiliated hospital in Shanghai were consecutively identified in this study. Demographics, disease related information, nutrition knowledge, attitude, and practice score were collected before gastrectomy. In addition, body weight before surgery (T0), body weight at one month (T1), two months (T2), and three months (T3) after gastrectomy were recorded. Generalized estimation equation was used to describe body weight change and analyze factors contributing to body weight change after surgery.ResultsThere were 49 patients recruited in the study. Patient body weight decreased by 9.2% at T1 (Wald χ = 271.173, P <0.001), 11.0% at T2 (Wald χ2 = 277.267, P <0.001), and 11.4% at T3 compared to baseline at T0 (Wald χ = 284.076, P <0.001). The results of GEE for multivariable analysis showed that surgery type (Wald χ = 6.027, P = 0.014) and preoperative BMI (Wald χ = 12.662, P = 0.005) were contributing factors of body weight change. Compared with distal gastrectomy patients, total gastrectomy patients experienced greater body weight loss (β = 2.8%, P = 0.014). Compared with patients with BMI&λτ; 18.5 kg/m2, patients with BMI ≥ 25 kg/m2experienced greater body weight loss (β = 4.5% P = 0.026).ConclusionGastric cancer patients experienced significant weight loss during 3 months after gastrectomy. Total gastrectomy and BMI ≥ 25 kg/m2were risk factors to postoperative body weight loss for GC patients. The results suggested hinted that clinician should pay attention to postoperative nutrition status of patient undergoing total gastrectomy and obesity patients. creator: Qiuju Tian creator: Liyuan Qin creator: Weiyi Zhu creator: Shaojie Xiong creator: Beiwen Wu uri: https://doi.org/10.7717/peerj.9390 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Tian et al.