title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1205 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Molecular characterization of two recombinant isolates of telosma mosaic virus infecting Passiflora edulis from Fujian Province in China link: https://peerj.com/articles/8576 last-modified: 2020-02-21 description: Telosma mosaic virus (TeMV) is an important plant virus causing considerable economic losses to passion fruit (Passiflora edulis) production worldwide, including China. In this study, the complete genome sequence (excluding the poly (A) tail) of two TeMV isolates, Fuzhou and Wuyishan, were determined to be 10,050 and 10,057 nucleotides, respectively. Sequence analysis indicated that Fuzhou and Wuyishan isolates share 78–98% nucleotide and 83–99% amino acid sequence identities with two TeMV isolates of Hanoi and GX, and a proposed new potyvirus, tentatively named PasFru. Phylogenetic analysis indicated that these TeMV isolates and PasFru were clustered into a monophyletic clade with high confidences. This indicated that PasFru and the four TeMV isolates should be considered as one potyvirus species. Two recombination breakpoints were identified within the CI and NIb genes of the Fuzhou isolate, and also within the P1 gene of the Wuyishan isolate. To the best of our knowledge, this is the first report of TeMV recombinants worldwide. creator: Lixue Xie creator: Fangluan Gao creator: Jianguo Shen creator: Xiaoyan Zhang creator: Shan Zheng creator: Lijie Zhang creator: Tao Li uri: https://doi.org/10.7717/peerj.8576 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Xie et al. title: Long non-coding RNA polymorphisms on 8q24 are associated with the prognosis of gastric cancer in a Chinese population link: https://peerj.com/articles/8600 last-modified: 2020-02-21 description: BackgroundGastric cancer (GC) remains the third leading cause of cancer death in China. Although genome-wide association studies have identified the association between several single nucleotide polymorphisms (SNPs) on 8q24 and the risk of GC, the role of these SNPs in the prognosis of GC in Chinese populations has not yet been fully evaluated. Therefore, this study was conducted to explore the association between long non-coding RNA (lncRNA) polymorphisms on 8q24 and the prognosis of GC.MethodsWe genotyped 726 surgically resected GC patients to explore the association between eight SNPs in the lncRNAs CCAT1 (rs10087719, rs7816475), PCAT1 (rs1026411), PRNCR1 (rs12682421, rs13252298), and CASC8 (rs1562430, rs4871789, rs6983267) transcribed from the 8q24 locus and the prognosis of GC in a Chinese population.ResultsWe found that the patients carrying rs12682421 AA genotypes survived for a shorter time than those with the GG/GA genotype (HR = 1.39, 95% confidence interval (CI) [1.09–1.78]). Compared with the CC/CT genotype, the TT genotype of rs1562430 was associated with an increased risk of death (HR = 1.38, 95% CI [1.06–1.80]). Furthermore, the results also identified the rs1026411 SNP as an independent prognostic factor for poor survival in GC patients. Patients carrying AA/AG variant genotypes had a 36% increased risk of death compared to those carrying the GG genotype (HR = 1.36, 95% CI [1.06–1.74]). These findings suggested that the rs12682421, rs1026411 and rs1562430 SNPs may contribute to the survival of GC and be prognostic markers for GC. creator: Yangyu Zhang creator: Yanhua Wu creator: Zhifang Jia creator: Donghui Cao creator: Na Yang creator: Yueqi Wang creator: Xueyuan Cao creator: Jing Jiang uri: https://doi.org/10.7717/peerj.8600 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhang et al. title: The complete mitogenome of Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Stylommatophora): mitochondrial genome architecture, evolution and phylogenetic considerations within Stylommatophora link: https://peerj.com/articles/8603 last-modified: 2020-02-21 description: Stylommatophora is one of the most speciose orders of Gastropoda, including terrestrial snails and slugs, some of which are economically important as human food, agricultural pests, vectors of parasites or due to invasiveness. Despite their great diversity and relevance, the internal phylogeny of Stylommatophora has been debated. To date, only 34 stylommatophoran mitogenomes were sequenced. Here, the complete mitogenome of an invasive pest slug, Arion vulgaris Moquin-Tandon, 1855 (Stylommatophora: Arionidae), was sequenced using next generation sequencing, analysed and compared with other stylommatophorans. The mitogenome of A. vulgaris measures 14,547 bp and contains 13 protein-coding, two rRNA, 22 tRNA genes, and one control region, with an A + T content of 70.20%. All protein coding genes (PCGs) are initiated with ATN codons except for COX1, ND5 and ATP8 and all are ended with TAR or T-stop codons. All tRNAs were folded into a clover-leaf secondary structure except for trnC and trnS1 (AGN). Phylogenetic analyses confirmed the position of A. vulgaris within the superfamily Arionoidea, recovered a sister group relationship between Arionoidea and Orthalicoidea, and supported monophyly of all currently recognized superfamilies within Stylommatophora except for the superfamily Helicoidea. Initial diversification time of the Stylommatophora was estimated as 138.55 million years ago corresponding to Early Cretaceous. The divergence time of A. vulgaris and Arion rufus (Linnaeus, 1758) was estimated as 15.24 million years ago corresponding to one of Earth’s most recent, global warming events, the Mid-Miocene Climatic Optimum. Furthermore, selection analyses were performed to investigate the role of different selective forces shaping stylommatophoran mitogenomes. Although purifying selection is the predominant selective force shaping stylommatophoran mitogenomes, six genes (ATP8, COX1, COX3, ND3, ND4 and ND6) detected by the branch-specific aBSREL approach and three genes (ATP8, CYTB and ND4L) detected by codon-based BEB, FUBAR and MEME approaches were exposed to diversifying selection. The positively selected substitutions at the mitochondrial PCGs of stylommatophoran species seems to be adaptive to environmental conditions and affecting mitochondrial ATP production or protection from reactive oxygen species effects. Comparative analysis of stylommatophoran mitogenome rearrangements using MLGO revealed conservatism in Stylommatophora; exceptions refer to potential apomorphies for several clades including rearranged orders of trnW-trnY and of trnE-trnQ-rrnS-trnM-trnL2-ATP8-trnN-ATP6-trnR clusters for the genus Arion. Generally, tRNA genes tend to be rearranged and tandem duplication random loss, transitions and inversions are the most basic mechanisms shaping stylommatophoran mitogenomes. creator: Özgül Doğan creator: Michael Schrödl creator: Zeyuan Chen uri: https://doi.org/10.7717/peerj.8603 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Doğan et al. title: The practicality of different eGFR equations in centenarians and near-centenarians: which equation should we choose? link: https://peerj.com/articles/8636 last-modified: 2020-02-21 description: BackgroundNo studies have examined the practicality of the Modification of Diet in Renal Disease (MDRD), Chronic Kidney Disease Epidemiological Collaboration (CKD-EPI) and Berlin Initiative Study 1 (BIS1) equations for the estimated glomerular filtration rate (eGFR) in a large sample of centenarians. We aim to investigate the differences among the equations and suggest the most suitable equation for centenarians and near-centenarians.MethodsA total of 966 centenarians and 787 near-centenarians were enrolled, and the eGFR was calculated using the three equations mentioned above. Agreement among the equations was investigated with the κ statistic and Bland–Altman plots. Sources of discrepancy were investigated using a partial correlation analysis.ResultsThe three equations for assessing eGFR are not considered interchangeable in centenarians and near-centenarians. Δ(MDRD, CKD-EPI) and Δ(MDRD, BIS1) increased with age, but Δ(CKD-EPI, BIS1) was relatively stable with age. Δ(MDRD, CKD-EPI) and Δ(MDRD, BIS1) were considerable in subjects with Scr levels less than 0.7 mg/dL and decreased with the Scr level. A considerable difference between CKD-EPI and BIS1 was observed for participants with Scr levels ranging from 0.5 to 1.5 mg/dL. This difference increased with Scr levels ranging from 0.5 to 0.7 mg/dL, was relatively stable for Scr levels ranging from 0.7 to 0.9 mg/dL, and decreased with Scr levels ranging from 0.9 to 1.5 mg/dL. The differences in the three comparisons were all greater in women than in men (p < 0.05).ConclusionsWe tend to suggest the MDRD equation to calculate the glomerular filtration rate (GFR) in elderly individuals >95 years old who have no risk factors for cardiovascular disease; the BIS1 equation to calculate the eGFR for elderly individuals younger than 94 years old who have risk factors for cardiovascular disease; the CKD-EPI equation to calculate the eGFR of elderly individuals with Scr levels greater than 1.5 mg/dL; and the BIS1 equation to calculate the eGFR of older women with Scr levels less than 0.7 mg/dL. creator: Qiuxia Han creator: Dong Zhang creator: Yali Zhao creator: Liang Liu creator: Jing Li creator: Fu Zhang creator: Fuxin Luan creator: Jiayu Duan creator: Zhangsuo Liu creator: Guangyan Cai creator: Xiangmei Chen creator: Hanyu Zhu uri: https://doi.org/10.7717/peerj.8636 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Han et al. title: Retrospective study: clinicopathological features and prognosis of idiopathic membranous nephropathy with seronegative anti-phospholipase A2 receptor antibody link: https://peerj.com/articles/8650 last-modified: 2020-02-21 description: BackgroundTo discuss the clinicopathological features and prognosis of patients with idiopathic membranous nephropathy (IMN) who are serum-negative for the anti-PLA2R antibody.MethodOverall, 229 IMN patients were retrospectively collected in this study and classified into anti-PLA2R antibody-negative (PLA2R−, 59 cases) and antibody-positive (PLA2R+, 170 cases) groups. The clinical and pathological features of the PLA2R− group were analyzed; 162 patients in both groups were followed up, and the PLA2R antigen was detected in renal biopsies from the PLA2R− group. Kaplan-Meier and survival analyses were used to compare differences in prognosis.ResultsSerum albumin levels were higher and 24-hour urine protein, creatinine, and beta 2-microglobulin (BMG) levels were lower in the PLA2R− group than in the PLA2R+ group; the proportion of acute and chronic tubular lesions was also significantly lower in the PLA2R− group than in in the PLA2R+ group. After treatment, the remission rate was significantly higher in the negative group than in the positive group (93.02% vs 74.78%,), especially the rate of complete remission (51.16% vs 23.47%). Furthermore, the PLA2R antigen-positive staining rate of 43 patients in the PLA2R− group was 62.79%. Although not significant, the survival rate was higher in the PLA2R− group than in the PLA2R+ group. BMG, 24-hour urine protein and acute and chronic tubular lesions were risk factors for kidney death, and 24-hour urine protein was an independent risk factor for kidney death.ConclusionsCompared with the PLA2R+ group, the PLA2R− group had mild clinical manifestations and pathological damage and a higher clinical treatment remission rate. Renal tissue PLA2R antigen testing can be considered for patients with seronegative IMN to increase the diagnostic rate. creator: Wenkai Guo creator: Yan Zhang creator: Caifeng Gao creator: Jing Huang creator: Jiatong Li creator: Rong Wang creator: Bing Chen uri: https://doi.org/10.7717/peerj.8650 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Guo et al. title: Transcriptome analysis of flavonoid biosynthesis in safflower flowers grown under different light intensities link: https://peerj.com/articles/8671 last-modified: 2020-02-21 description: BackgroundSafflower (Carthamus tinctorius L.) is a domesticated species with a long history of cultivation and widespread distribution across the globe, and light plays an important role in controlling its distribution boundary. Flowers from safflower have been widely used in traditional Chinese medicine because of their ability to improve cerebral blood flow. Flavonoids are the main active compounds in safflower and have many pharmacological effects. In this study, we aimed to explore the relationship between different light intensities and flavonoid biosynthesis in safflower flowers cultivated in greenhouse.MethodsThe transcriptome of safflower flowers grown under different light intensities were sequenced through BGISEQ-500 platform. After assembled and filtered, Unigenes were annotated by aligning with seven functional databases. Differential expression analysis of two samples was performed with the DEseq2 package. Differentially expressed genes (DEGs) related with flavonoids biosynthesis were analyzed by Real-time PCR (RT-PCR). Flavonoids accumulation in flowers were determined by high performance liquid chromatography and spectrophotometer.ResultsTranscriptome analysis of safflower flowers cultivated under different light intensities was performed. A total of 99.16 Gb data were obtained, and 78,179 Unigenes were annotated. Among the DEGs, 13 genes were related to flavonoid biosynthesis. The differential expressions of seven key genes were confirmed by RT-PCR. In addition, the levels of some flavonoids were measured in safflower flowers grown under different light intensities. CtHCT3 gene expression showed a significantly negative correlation with kaempferol content in safflower grown under different light intensities.ConclusionOur results strongly suggested that the reduction in light intensity in a suitable range promoted flavonoid biosynthesis in safflower flowers. We suggest that the expressions of HCT genes played an important role in flavonoid accumulation in safflower flowers. Our study lays a foundation for further research on the effects of light on flavonoid biosynthesis in safflower. creator: Chaoxiang Ren creator: Jie Wang creator: Bin Xian creator: Xiaohui Tang creator: Xuyun Liu creator: Xueli Hu creator: Zunhong Hu creator: Yiyun Wu creator: Cuiping Chen creator: Qinghua Wu creator: Jiang Chen creator: Jin Pei uri: https://doi.org/10.7717/peerj.8671 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ren et al. title: Recent update in diagnosis and treatment of human pythiosis link: https://peerj.com/articles/8555 last-modified: 2020-02-20 description: Human pythiosis is an infectious condition with high morbidity and mortality. The causative agent is the oomycete microorganism Pythium insidiosum. The pathogen inhabits ubiquitously in a wet environment, and direct exposure to the pathogen initiates the infection. Most patients with pythiosis require surgical removal of the affected organ, and many patients die from the disease. Awareness of pythiosis among healthcare personnel is increasing. In this review, we summarized and updated information on the diagnosis and treatment of human pythiosis. Vascular and ocular pythiosis are common clinical manifestations. Recognition of the typical clinical features of pythiosis is essential for early diagnosis. The definitive diagnosis of the disease requires laboratory testing, such as microbiological, serological, molecular, and proteomic assays. In vascular pythiosis, surgical intervention to achieve the organism-free margin of the affected tissue, in combination with the use of antifungal drugs and P. insidiosum immunotherapy, remains the recommended treatment. Ocular pythiosis is a serious condition and earliest therapeutic penetrating keratoplasty with wide surgical margin is the mainstay treatment. Thorough clinical assessment is essential in all patients to evaluate the treatment response and detect an early sign of the disease recurrence. In conclusion, early diagnosis and proper management are the keys to an optimal outcome of the patients with pythiosis. creator: Maria Nina Chitasombat creator: Passara Jongkhajornpong creator: Kaevalin Lekhanont creator: Theerapong Krajaejun uri: https://doi.org/10.7717/peerj.8555 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Chitasombat et al. title: The effects of phylogeny, body size, and locomotor behavior on the three-dimensional shape of the pelvis in extant carnivorans link: https://peerj.com/articles/8574 last-modified: 2020-02-20 description: The mammalian pelvis is thought to exhibit adaptations to the functional demands of locomotor behaviors. Previous work in primates has identified form-function relationships between pelvic shape and locomotor behavior; few studies have documented such relationships in carnivorans, instead focusing on long bones. Most work on the functional morphology of the carnivoran pelvis, in particular, has used univariate measures, with only a few previous studies incorporating a three-dimensional (3D) analysis. Here we test the hypothesis that carnivoran taxa that are characterized by different locomotor modes also differ in 3D shape of the os coxae. Using 3D geometric morphometrics and phylogenetic comparative methods, we evaluate the phylogenetic, functional, and size-related effects on 3D pelvis shape in a sample of 33 species of carnivorans. Using surface models derived from laser scans, we collected a suite of landmarks (N = 24) and curve semilandmarks (N = 147). Principal component analysis on Procrustes coordinates demonstrates patterns of shape change in the ischiopubis and ilium likely related to allometry. Phylogenetic generalized least squares analysis on principal component scores demonstrates that phylogeny and body size have greater effects on pelvic shape than locomotor function. Our results corroborate recent research finding little evidence of locomotor specialization in the pelvis of carnivorans. More research on pelvic morphological integration and evolvability is necessary to understand the factors driving pelvic evolution in carnivorans. creator: Kristi L. Lewton creator: Ryan Brankovic creator: William A. Byrd creator: Daniela Cruz creator: Jocelyn Morales creator: Serin Shin uri: https://doi.org/10.7717/peerj.8574 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Lewton et al. title: Effects of manganese and zinc on the growth process of Phytophthora nicotianae and the possible inhibitory mechanisms link: https://peerj.com/articles/8613 last-modified: 2020-02-20 description: BackgroundPhytophthora nicotianae is a fungal soil-borne pathogen that damages various plant species. Mancozeb and Zineb, fungicides containing manganese (Mn) and zinc (Zn) as the main components, are widely used to control the diseases caused by Phytophthora. However, the inhibition mechanism is still unclear. The purpose of this study was to examine the effects of Mn and Zn on P. nicotianae and to determine possible inhibitory mechanisms of Mn and Zn on sporangiogenesis of P. nicotianae.MethodsThe mycelial growth, sporangium generation, zoosporogenesis and zoospore germination of P. nicotianae were observed under Mn and Zn treatments. The gene (csn4 and csn7) expression levels of P. nicotianae in different growth stages were examined. Csn4 and csn7 gene expression, superoxide dismutase (SOD) activity, catalase (CAT) activity and malondialdehyde (MDA) content were tested at the stage of sporangiogenesis under different Mn and Zn concentrations.ResultsMycelial growth of P. nicotianae was significantly inhibited by Mn from ≥1 mg/L concentration and by Zn from ≥10 mg/L. The sporangia production, sporangia release, and zoospore germination of P. nicotianae were significantly reduced by Mn at all concentrations, while treatment with Zn from ≥0.5 mg/L concentration significantly inhibited the same processes. At the same concentration, the inhibition rate of Mn on the growth process of P. nicotianae was higher than that of Zn. The csn4 and csn7 gene transcription of P. nicotianae were significantly reduced by all treatments with Mn and Zn at the stage of sporangiogenesis. With the increase of Mn concentration, the activities of SOD and CAT increased to maxima and then decreased, and the content of MDA gradually increased during sporangiogenesis of P. nicotianae. The sporangia production of P. nicotianae was significantly positively correlated with the expression levels of the genes csn4 and csn7.ConclusionThe inhibitory effect of Mn on the growth process of P. nicotianae was stronger than that of Zn, especially on sporangiogenesis and zoosporogenesis. A possible mechanism of the inhibitory effect on sporangiogenesis of P. nicotianae was that Mn and Zn acted by inhibiting the expression levels of the genes csn4 and csn7 and by affecting antioxidant enzyme activity (further resulting in lipid peroxidation) in the sporangium of P. nicotianae. creator: Yifang Luo creator: Aimei Yao creator: Mouyi Tan creator: Zhenlun Li creator: Ling Qing creator: Shuiying Yang uri: https://doi.org/10.7717/peerj.8613 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Luo et al. title: Multidimensional evaluation of the TRMM 3B43V7 satellite-based precipitation product in mainland China from 1998–2016 link: https://peerj.com/articles/8615 last-modified: 2020-02-20 description: This study evaluates the applicability of the Tropical Rain Measurement Mission (TRMM) 3B43V7 product for use throughout mainland China. Four statistical metrics were used based on the observations made by rain gauges; these metrics were the correlation coefficient (R), the relative bias (RB), the root mean square error (RMSE) and Nash-Sutcliffe efficiency (NSE), and they were chosen to evaluate the performance of the 3B43V7 product at temporal and spatial scales. The results revealed that 3B43V7 performed satisfactorily on all timescales (R > 0.9 and NSE > 0.86); however, it overestimated the results when compared with the rain gauge observations in certain circumstances (RB = 9.7%). Monthly estimates from 3B43V7 were in agreement with rain gauge observations. 3B43V7 can effectively capture the seasonal patterns of precipitation characteristics over mainland China. However, 3B43V7 tends to register a greater overestimation of precipitation in the winter (RB = 14%) than in other seasons while showing greater consistency with the observations made by rain gauges during dry periods. The 3B43V7 product performs well in the eastern part of mainland China, while its performance is poor in the western part of mainland China. In terms of altitude, 3B43V7 performs satisfactorily in areas with moderate to low altitudes (when altitude < 3,500 m, R > 0.9, NSE > 0.8 and RB < 10.2%) but RB values increase with altitude. Overall, 3B43V7 had a favorable performance throughout mainland China. creator: Ziteng Zhou creator: Bin Guo creator: Youzhe Su creator: Zhongsheng Chen creator: Juan Wang uri: https://doi.org/10.7717/peerj.8615 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhou et al.