title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1083 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Transcriptomic analysis reveals ethylene signal transduction genes involved in pistil development of pumpkin link: https://peerj.com/articles/9677 last-modified: 2020-08-18 description: Development of female flowers is an important process that directly affects the yield of Cucubits. Little information is available on the sex determination and development of female flowers in pumpkin, a typical monoecious plant. In the present study, we used aborted and normal pistils of pumpkin for RNA-Seq analysis and determined the differentially expressed genes (DEGs) to gain insights into the molecular mechanism underlying pistil development in pumpkin. A total of 3,817 DEGs were identified, among which 1,341 were upregulated and 2,476 were downregulated. The results of transcriptome analysis were confirmed by real-time quantitative RT-PCR. KEGG enrichment analysis showed that the DEGs were significantly enriched in plant hormone signal transduction and phenylpropanoid biosynthesis pathway. Eighty-four DEGs were enriched in the plant hormone signal transduction pathway, which accounted for 12.54% of the significant DEGs, and most of them were annotated as predicted ethylene responsive or insensitive transcription factor genes. Furthermore, the expression levels of four ethylene signal transduction genes in different flower structures (female calyx, pistil, male calyx, stamen, leaf, and ovary) were investigated. The ethyleneresponsive DNA binding factor, ERDBF3, and ethylene responsive transcription factor, ERTF10, showed the highest expression in pistils and the lowest expression in stamens, and their expression levels were 78- and 162-times more than that in stamens, respectively. These results suggest that plant hormone signal transduction genes, especially ethylene signal transduction genes, play an important role in the development of pistils in pumpkin. Our study provides a theoretical basis for further understanding of the mechanism of regulation of ethylene signal transduction genes in pistil development and sex determination in pumpkin. creator: Qingfei Li creator: Li Zhang creator: Feifei Pan creator: Weili Guo creator: Bihua Chen creator: Helian Yang creator: Guangyin Wang creator: Xinzheng Li uri: https://doi.org/10.7717/peerj.9677 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Behavioural variability among captive African elephants in the use of the trunk while feeding link: https://peerj.com/articles/9678 last-modified: 2020-08-18 description: The Proboscideans, an order of mammals including elephants, are the largest of the Earth lands animals. One probable consequence of the rapid increase of their body size is the development of the trunk, a multitask highly sensitive organ used in a large repertoire of behaviours. The absence of bones in the trunk allows a substantial degree of freedom for movement in all directions, and this ability could underlie individual-level strategies. We hypothesised a stronger behavioural variability in simple tasks, and a correlation between the employed behaviours and the shape and size of the food. The observations of a captive group of African elephants allowed us to create a complete catalogue of trunk movements in feeding activities. We noted manipulative strategies and impact of food item properties on the performed behaviours. The results show that a given item is manipulated with a small panel of behaviours, and some behaviours are specific to a single shape of items. The study of the five main feeding behaviours emphasises a significant variability between the elephants. Each individual differed from every other individual in the proportion of at least one behaviour, and every behaviour was performed in different proportions by the elephants. Our findings suggest that during their lives elephants develop individual strategies adapted to the manipulated items, which increases their feeding efficiency. creator: Maëlle Lefeuvre creator: Patrick Gouat creator: Baptiste Mulot creator: Raphaël Cornette creator: Emmanuelle Pouydebat uri: https://doi.org/10.7717/peerj.9678 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Lefeuvre et al. title: The vaginal microbiome of sub-Saharan African women: revealing important gaps in the era of next-generation sequencing link: https://peerj.com/articles/9684 last-modified: 2020-08-18 description: Accurate characterization of the vaginal microbiome remains a fundamental goal of the Human Microbiome project (HMP). For over a decade, this goal has been made possible deploying high-throughput next generation sequencing technologies (NGS), which indeed has revolutionized medical research and enabled large-scale genomic studies. The 16S rRNA marker-gene survey is the most commonly explored approach for vaginal microbial community studies. With this approach, prior studies have elucidated substantial variations in the vaginal microbiome of women from different ethnicities. This review provides a comprehensive account of studies that have deployed this approach to describe the vaginal microbiota of African women in health and disease. On the basis of published data, the few studies reported from the African population are mainly in non-pregnant post pubertal women and calls for more detailed studies in pregnant and postnatal cohorts. We provide insight on the use of more sophisticated cutting-edge technologies in characterizing the vaginal microbiome. These technologies offer high-resolution detection of vaginal microbiome variations and community functional capabilities, which can shed light into several discrepancies observed in the vaginal microbiota of African women in an African population versus women of African descent in the diaspora. creator: Nkechi Martina Odogwu creator: Oladapo O. Olayemi creator: Akinyinka O. Omigbodun uri: https://doi.org/10.7717/peerj.9684 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Odogwu et al. title: Fan worms (Annelida: Sabellidae) from Indonesia collected by the Snellius II Expedition (1984) with descriptions of three new species and tube microstructure link: https://peerj.com/articles/9692 last-modified: 2020-08-18 description: The Indonesian archipelago is one of the most diverse regions in the marine World. Many contributions on polychaete worms have been published since the Dutch Siboga Expedition to the Indonesian archipelago at the end of the 19th century. In this study, we examined specimens of Sabellidae Latreille, 1825 collected during the Snellius II Expedition (1984) to Indonesia, carried out by the Dutch Research Vessel (RV) “Tyro” and the Indonesian RV “Samudera”. The results include reports of Acromegalomma acrophthalmos, A. interruptum, A. sp., Bispira manicata, B. porifera, B. secusoluta, Branchiomma boholense, Notaulax pyrrohogaster, N. tenuitorques, N. sp. 3, Parasabella crassichaetae, Perkinsiana anodina, and Sabellastarte spectabilis. In addition, three new species are described: Acromegalomma sumbense sp. nov., Claviramus olivager sp. nov., and Notaulax montiporicola sp. nov., the latter in living coral (Montipora nodosa). Further, Sabella (Potamilla) polyophthalmos Grube is transferred to Pseudopotamilla. Additional histological accounts of B. porifera and tube microstructure of A. acrophthalmos, B. porifera, P. anodina, Pseudopotamilla polyophthalmos and Sabellastarte spectabilis are also included. creator: María Ana Tovar-Hernández creator: Harry A. ten Hove creator: Olev Vinn creator: Michał Zatoń creator: Jesús Angel de León-González creator: María Elena García-Garza uri: https://doi.org/10.7717/peerj.9692 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Tovar-Hernández et al. title: Transcriptome analysis provides a blueprint of coral egg and sperm functions link: https://peerj.com/articles/9739 last-modified: 2020-08-18 description: BackgroundReproductive biology and the evolutionary constraints acting on dispersal stages are poorly understood in many stony coral species. A key piece of missing information is egg and sperm gene expression. This is critical for broadcast spawning corals, such as our model, the Hawaiian species Montipora capitata, because eggs and sperm are exposed to environmental stressors during dispersal. Furthermore, parental effects such as transcriptome investment may provide a means for cross- or trans-generational plasticity and be apparent in egg and sperm transcriptome data.MethodsHere, we analyzed M. capitata egg and sperm transcriptomic data to address three questions: (1) Which pathways and functions are actively transcribed in these gametes? (2) How does sperm and egg gene expression differ from adult tissues? (3) Does gene expression differ between these gametes?ResultsWe show that egg and sperm display surprisingly similar levels of gene expression and overlapping functional enrichment patterns. These results may reflect similar environmental constraints faced by these motile gametes. We find significant differences in differential expression of egg vs. adult and sperm vs. adult RNA-seq data, in contrast to very few examples of differential expression when comparing egg vs. sperm transcriptomes. Lastly, using gene ontology and KEGG orthology data we show that both egg and sperm have markedly repressed transcription and translation machinery compared to the adult, suggesting a dependence on parental transcripts. We speculate that cell motility and calcium ion binding genes may be involved in gamete to gamete recognition in the water column and thus, fertilization. creator: Julia Van Etten creator: Alexander Shumaker creator: Tali Mass creator: Hollie M. Putnam creator: Debashish Bhattacharya uri: https://doi.org/10.7717/peerj.9739 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2020 Van Etten et al. title: Gender-specific associations between apolipoprotein A1 and arterial stiffness in patients with nonalcoholic fatty liver disease link: https://peerj.com/articles/9757 last-modified: 2020-08-18 description: BackgroundLipid metabolism factors may play an important role in the progression of nonalcoholic fatty liver disease (NAFLD) and its related cardiovascular dysfunctions. The study aims to assess whether Apolipoprotein A-1 (ApoA1) was associated with vascular stiffness in NAFLD patients.MethodsFrom 2012 to 2013, we included 2,295 non-alcohol users with fatty liver disease (1,306 male patients) and completely excluded subjects who drank any alcohol ever to eliminate the effect of alcohol intake. The serum ApoA1 levels and the brachial-ankle pulse wave velocity (baPWV) were measured.ResultsThe baPWV in men was much higher than in female patients (1,412.79 cm/s vs. 1,358.69 cm/s, P < 0.001). ApoA1 level was positively associated with baPWV odd ratio (OR), 4.18; 95% confidence interval (CI) [1.16–15.1], P < 0.05) in patients with AST/ALT < 1 and (OR, 4.70; 95% CI [1.36–16.23], P < 0.05) in patients with AST/ALT ≥ 1 respectively. Only arterial stiffness in men was associated with ApoA1 (OR, 3.96; 95% CI [1.29–12.30], P < 0.05) in logistics regression models adjusted for age, gender, body mass index, education attainment, physical activity, smoking, history of hypertension and high-density lipoprotein. The relationship between ApoA1 and baPWV in male NAFLD patients remained significant (confidence, 156.42; 95% CI [49.34–263.50], P < 0.05) in the fully adjusted linear regression model.ConclusionThe serum ApoA1 was associated with arterial stiffness in male NAFLD patients. Increased ApoA1 level should be considered as an independent risk factor for arterial stiffness in male NAFLD patients, suggesting that NAFLD may alter arterial stiffness by “ApoA1-related” mechanism in men. creator: Xulong Sun creator: Ruifang Chen creator: Guangyu Yan creator: Zhiheng Chen creator: Hong Yuan creator: Wei Huang creator: Yao Lu uri: https://doi.org/10.7717/peerj.9757 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Sun et al. title: Significance of hub genes and immune cell infiltration identified by bioinformatics analysis in pelvic organ prolapse link: https://peerj.com/articles/9773 last-modified: 2020-08-18 description: ObjectivePelvic organ prolapse (POP) refers to the decline of pelvic organ position and dysfunction caused by weak pelvic floor support. The aim of the present study was to screen the hub genes and immune cell infiltration related to POP disease.MethodsMicroarray data of 34 POP tissues in the GSE12852 gene expression dataset were used as research objects. Weighted gene co-expression network analysis (WGCNA) was performed to elucidate the hub module and hub genes related to POP occurrence. Gene function annotation was performed using the DAVID tool. Differential analysis based on the GSE12852 dataset was carried out to explore the expression of the selected hub genes in POP and non-POP tissues, and RT-qPCR was used to validate the results. The differential immune cell infiltration between POP and non-POP tissues was investigated using the CIBERSORT algorithm.ResultsWGCNA revealed the module that possessed the highest correlation with POP occurrence. Functional annotation indicated that the genes in this module were mainly involved in immunity. ZNF331, THBS1, IFRD1, FLJ20533, CXCR4, GEM, SOD2, and SAT were identified as the hub genes. Differential analysis and RT-qPCR demonstrated that the selected hub genes were overexpressed in POP tissues as compared with non-POP tissues. The CIBERSORT algorithm was employed to evaluate the infiltration of 22 immune cell types in POP tissues and non-POP tissues. We found greater infiltration of activated mast cells and neutrophils in POP tissues than non-POP tissues, while the infiltration of resting mast cells was lower in POP tissues. Moreover, we investigated the relationship between the type of immune cell infiltration and hub genes by Pearson correlation analysis. The results indicate that activated mast cells and neutrophils had a positive correlation with the hub genes, while resting mast cells had a negative correlation with the hub genes.ConclusionsOur research identified eight hub genes and the infiltration of three types of immune cells related to POP occurrence. These hub genes may participate in the pathogenesis of POP through the immune system, giving them a certain diagnostic and therapeutic value. creator: Ying Zhao creator: Zhijun Xia creator: Te Lin creator: Yitong Yin uri: https://doi.org/10.7717/peerj.9773 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zhao et al. title: CMTM6 significantly relates to PD-L1 and predicts the prognosis of gastric cancer patients link: https://peerj.com/articles/9536 last-modified: 2020-08-17 description: BackgroundThe CKLF-like MARVEL transmembrane domain containing 6 (CMTM6) is a key regulator of the programed death receptor ligand-1 (PD-L1) protein. However, the usefulness of CMTM6 expression as a prognostic indicator and the relationship between CMTM6 and PD-L1 expression in gastric cancer (GC) remains unclear.ObjectivesWe evaluated the expression and prognostic implications of CMTM6 in GC tissue and its relationship with PD-L1 expression.Patients and methodsThe protein expressions of CMTM6 and PD-L1 were detected in 122 cases of postoperative GC tissue using immunohistochemical (IHC) assays. Kaplan–Meier survival analysis was used to calculate the survival probability and a log-rank test was used to compare the survival curves. Univariate and multivariate Cox proportional hazard regression analyses were used to evaluate the clinically-related factors associated with survival. Pearson’s correlation was used to determine the correlation analysis and estimate the statistical significance. The univariate and multivariate logistic regression analyses were used to analyze the relationship between clinically-related factors and PD-L1 expression.ResultsKaplan–Meier survival analysis showed that patients with high CMTM6 expression had shorter overall survival (OS) than those with low expression (P < 0.001). The expression of CMTM6 was an independent risk factor for prognosis in multivariate Cox proportional hazard regression analyses (HR:2.221, CI% [1.36–3.628], P = 0.001). The OS of patients with positively expressed PD-L1 was significantly shorter than those with negatively expressed PD-L1 (P = 0.003). The expression of CMTM6 was significantly related to the positive expression of PD-L1 in gastric cancer tissues (r = 0.186, P = 0.041). The expression of CMTM6 was the independent risk factor for PD-L1 expression in multivariate logistic regression analysis (OR:2.538, CI% [1.128–5.714], P = 0.024).ConclusionCMTM6 expression is significantly related to PD-L1 and may be a useful prognostic indicator and a specific therapeutic target for cancer immunotherapy for GC patients. creator: Xin Li creator: Ling Chen creator: Chuan Gu creator: Qiaoli Sun creator: Jia Li uri: https://doi.org/10.7717/peerj.9536 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Li et al. title: Determination of fitness traits of Orius strigicollis Poppius (Hemiptera: Anthocoridae) on Pectinophora gossypiella (Lepidoptera: Gelechiidae) using two-sex life table analysis link: https://peerj.com/articles/9594 last-modified: 2020-08-17 description: BackgroundPink bollworm (Pectinophora gossypiella) is a destructive insect pest of cotton crops in China and globally, which is actively predated on by Orius strigicollis. Studies on the fitness or survival of O. strigicollis fed on P. gossypiella at different temperatures have not been reported. The fitness of O. strigicollis may be well explained using two-sex life table parameters. Thus, the present study provides important insights for the effective biocontrol of P. gossypiella.MethodologyConsidering the importance of fitness parameters and biocontrol, the present study explores the feeding potential and age-stage, two-sex life table traits of O. strigicollis on P. gossypiella eggs at different temperatures (24, 28 and 32 °C) in the laboratory.ResultsThe intrinsic rate of increase (r) was higher at 28 °C (0.14 d−1) than at 24 °C (0.0052 d−1) and 32 °C (0.12 d−1). Similarly, the net reproductive rate (R0) was higher at 28 °C (17.63 offspring) than at 24 °C (1.13 offspring) and 32 °C (10.23 offspring). This concluded that the maximum feeding potential and growth capacity of O. strigicollis could be attained at 28 °C when fed on P. gossypiella eggs. O. strigicollis adults preferred to feed on P. gossypiella eggs compared with first instar larvae. Based on these results, the present study suggests that O. strigicollis represents a promising biological control agent against P. gossypiella eggs in cotton fields. creator: Shahzaib Ali creator: Qian Zhu creator: Waqar Jaleel creator: Shakeel Ur Rehman creator: Muhammad Asim Rasheed creator: Muhammad Musa Khan creator: Yasir Islam creator: Muhammad Hafeez creator: Xingmiao Zhou uri: https://doi.org/10.7717/peerj.9594 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Ali et al. title: Microbiome dynamics in the tissue and mucus of acroporid corals differ in relation to host and environmental parameters link: https://peerj.com/articles/9644 last-modified: 2020-08-17 description: Corals are associated with diverse microbial assemblages; however, the spatial-temporal dynamics of intra-species microbial interactions are poorly understood. The coral-associated microbial community varies substantially between tissue and mucus microhabitats; however, the factors controlling the occurrence, abundance, and distribution of microbial taxa over time have rarely been explored for different coral compartments simultaneously. Here, we test (1) differentiation in microbiome diversity and composition between coral compartments (surface mucus and tissue) of two Acropora hosts (A. tenuis and A. millepora) common along inshore reefs of the Great Barrier Reef, as well as (2) the potential linkage between shifts in individual coral microbiome families and underlying host and environmental parameters. Amplicon based 16S ribosomal RNA gene sequencing of 136 samples collected over 14 months, revealed significant differences in bacterial richness, diversity and community structure among mucus, tissue and the surrounding seawater. Seawater samples were dominated by members of the Synechococcaceae and Pelagibacteraceae bacterial families. The mucus microbiome of Acropora spp. was dominated by members of Flavobacteriaceae, Synechococcaceae and Rhodobacteraceae and the tissue was dominated by Endozoicimonaceae. Mucus microbiome in both Acropora species was primarily correlated with seawater parameters including levels of chlorophyll a, ammonium, particulate organic carbon and the sum of nitrate and nitrite. In contrast, the correlation of the tissue microbiome to the measured environmental (i.e., seawater parameters) and host health physiological factors differed between host species, suggesting host-specific modulation of the tissue-associated microbiome to intrinsic and extrinsic factors. Furthermore, the correlation between individual coral microbiome members and environmental factors provides novel insights into coral microbiome-by-environment dynamics and hence has potential implications for current reef restoration and management efforts (e.g. microbial monitoring and observatory programs). creator: Giulia M. Marchioro creator: Bettina Glasl creator: Aschwin H. Engelen creator: Ester A. Serrão creator: David G. Bourne creator: Nicole S. Webster creator: Pedro R. Frade uri: https://doi.org/10.7717/peerj.9644 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Marchioro et al.