title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1382 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Pituitary tissue-specific miR-7a-5p regulates FSH expression in rat anterior adenohypophyseal cells link: https://peerj.com/articles/6458 last-modified: 2019-04-09 description: The follicle-stimulating hormone (FSH), which is synthesized and secreted by the anterior pituitary gland, plays an important role in regulating reproductive processes. In this study, using the TargetScan program, we predicted that microRNAs (miRNAs) regulate FSH secretion. Dual-luciferase reporter assays were performed and identified miR-7a-5p. MiR-7a-5p has been reported to regulate diverse cellular functions. However, it is unclear whether miR-7a-5p binds to mRNAs and regulates reproductive functions. Therefore, we constructed a suspension of rat anterior pituitary cells and cultured them under adaptive conditions, transfected miR-7a-5p mimics or inhibitor into the cell suspension and detected expression of the FSHb gene. The results demonstrated that miR-7a-5p downregulated FSHb expression levels, while treatment with miR-7a-5p inhibitors upregulated FSHb expression levels relative to those of negative control groups, as shown by quantitative PCR analysis. The results were confirmed with a subsequent experiment showing that FSH secretion was reduced after treatment with mimics and increased in the inhibitor groups, as shown by enzyme-linked immunosorbent assay. Our results indicated that miR-7a-5p downregulates FSHb expression levels, resulting in decreased FSH synthesis and secretion, which demonstrates the important role of miRNAs in the regulation of FSH and animal reproduction. creator: Chang-Jiang Wang creator: Hai-Xiang Guo creator: Dong-Xu Han creator: Ze-Wen Yu creator: Yi Zheng creator: Hao Jiang creator: Yan Gao creator: Bao Yuan creator: Jia-Bao Zhang uri: https://doi.org/10.7717/peerj.6458 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al. title: Transcriptional profiling in the livers of rats after hypobaric hypoxia exposure link: https://peerj.com/articles/6499 last-modified: 2019-04-09 description: Ascent to high altitude feels uncomfortable in part because of a decreased partial pressure of oxygen due to the decrease in barometric pressure. The molecular mechanisms causing injury in liver tissue after exposure to a hypoxic environment are widely unknown. The liver must physiologically and metabolically change to improve tolerance to altitude-induced hypoxia. Since the liver is the largest metabolic organ and regulates many physiological and metabolic processes, it plays an important part in high altitude adaptation. The cellular response to hypoxia results in changes in the gene expression profile. The present study explores these changes in a rat model. To comprehensively investigate the gene expression and physiological changes under hypobaric hypoxia, we used genome-wide transcription profiling. Little is known about the genome-wide transcriptional response to acute and chronic hypobaric hypoxia in the livers of rats. In this study, we carried out RNA-Sequencing (RNA-Seq) of liver tissue from rats in three groups, normal control rats (L), rats exposed to acute hypobaric hypoxia for 2 weeks (W2L) and rats chronically exposed to hypobaric hypoxia for 4 weeks (W4L), to explore the transcriptional profile of acute and chronic mountain sickness in a mammal under a controlled time-course. We identified 497 differentially expressed genes between the three groups. A principal component analysis revealed large differences between the acute and chronic hypobaric hypoxia groups compared with the control group. Several immune-related and metabolic pathways, such as cytokine-cytokine receptor interaction and galactose metabolism, were highly enriched in the KEGG pathway analysis. Similar results were found in the Gene Ontology analysis. Cogena analysis showed that the immune-related pathways were mainly upregulated and enriched in the acute hypobaric hypoxia group. creator: Zhenguo Xu creator: Zhilong Jia creator: Jinlong Shi creator: Zeyu Zhang creator: Xiaojian Gao creator: Qian Jia creator: Bohan Liu creator: Jixuan Liu creator: Chunlei Liu creator: Xiaojing Zhao creator: Kunlun He uri: https://doi.org/10.7717/peerj.6499 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Xu et al. title: Maturation trade-offs in octopus females and their progeny: energy, digestion and defence indicators link: https://peerj.com/articles/6618 last-modified: 2019-04-09 description: Sexual maturation and reproduction influence the status of a number of physiological processes and consequently the ecology and behaviour of cephalopods. Using Octopus mimus as a study model, the present work was focused in the changes in biochemical compound and activity that take place during gonadal maturation of females and its consequences in embryo and hatchlings characteristics. To do that, a total of 31 adult females of O. mimus were sampled to follow metabolites (ovaries and digestive gland) and digestive enzyme activities (alkaline and acidic proteases) during physiological and functional maturation. Levels of protein (Prot), triacylglyceride (TG), cholesterol (Chol), glucose (Glu), and glycogen (Gly) were evaluated. Groups of eggs coming from mature females were also sampled along development and after hatching (paralarvae of 1 and 3 days old) to track metabolites (Prot, TG, Glu, Gly, TG, Chol), digestive enzymes activity (Lipase, alkaline proteases, and acidic proteases), and antioxidant/detoxification defence indicators with embryos development. Based on the data obtained, we hypothesized that immature females store Chol in their ovaries, probably from the food they ingested, but switch to TG reserves at the beginning of the maturation processes. At the same time, results suggest that these processes were energetically supported by Glu, obtained probably from Gly breakdown by gluconeogenic pathways. Also, was observed that embryos metabolites and enzyme activities (digestive and antioxidant/detoxification enzymes) where maintained without significant changes and in a low activity during the whole organogenesis, meaning that organogenesis is relatively not energetically costly. In contrast, after organogenesis, a mobilization of nutrients and activation of the metabolic and digestive enzymes was observed, together with increments in consumption of yolk and Gly, and reduction in lipid peroxidation. Derived from our results, we also have the hypothesis that reactive oxygen species (ROS) were produced during the metabolic processes that occurs in ovarian maturation. Those ROS may be in part transferred to the egg provoking a ROS charge to the embryos. The elimination of ROS in embryos started when the activity of the heart and the absorption of the yolk around stages XIV and XV were evident. Altogether, these processes allowed the paralarvae to hatch with buffered levels of ROS and with the antioxidant defence mechanisms ready to support further ROS production derived from paralarvae higher life stage requirements (feeding and metabolic demands). creator: Alberto Olivares creator: Gabriela Rodríguez-Fuentes creator: Maite Mascaró creator: Ariadna Sanchez Arteaga creator: Karen Ortega creator: Claudia Caamal Monsreal creator: Nelly Tremblay creator: Carlos Rosas uri: https://doi.org/10.7717/peerj.6618 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Olivares et al. title: Evidence for an oncogenic role of HOXC6 in human non-small cell lung cancer link: https://peerj.com/articles/6629 last-modified: 2019-04-09 description: BackgroundIdentification of specific biomarkers is important for the diagnosis and treatment of non-small cell lung cancer (NSCLC). HOXC6 is a homeodomain-containing transcription factor that is highly expressed in several human cancers; however, its role in NSCLC remains unknown.MethodsThe expression and protein levels of HOXC6 were assessed in NSCLC tissue samples by Quantitative real-time PCR (qRT-PCR) and immunohistochemistry, respectively. HOXC6 was transfected into the NSCLC cell lines A549 and PC9, and used to investigate its effect on proliferation, migration, and invasion using CFSE, wound healing, and Matrigel invasion assays. Next-generation sequencing was also used to identify downstream targets of HOXC6 and to gain insights into the molecular mechanisms underlying its biological function.ResultsHOXC6 expression was significantly increased in 66.6% (20/30) of NSCLC tumor samples in comparison to normal controls. HOXC6 promoted proliferation, migration, and invasion of NSCLC cells in vitro. RNA-seq analysis demonstrated the upregulation of 310 and 112 genes in A549-HOXC6 and PC9-HOXC6 cells, respectively, and the downregulation of 665 and 385 genes in A549-HOXC6 and PC9-HOXC6 cells, respectively. HOXC6 was also found to regulate the expression of genes such as CEACAM6, SPARC, WNT6, CST1, MMP2, and KRT13, which have documented pro-tumorigenic functions.DiscussionHOXC6 is highly expressed in NSCLC, and it may enhance lung cancer progression by regulating the expression of pro-tumorigenic genes involved in proliferation, migration, and invasion. Our study highlighted the oncogenic potential of HOXC6, and suggests that it may be a novel biomarker for the diagnosis and treatment of NSCLC. creator: Yingcheng Yang creator: Xiaoping Tang creator: Xueqin Song creator: Li Tang creator: Yong Cao creator: Xu Liu creator: Xiaoyan Wang creator: Yan Li creator: Minglan Yu creator: Haisu Wan creator: Feng Chen uri: https://doi.org/10.7717/peerj.6629 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Yang et al. title: From climate zone to microhabitat—environmental factors affecting the coastal distribution of tiger beetles (Coleoptera: Cicindelidae) in the south-eastern European biodiversity hotspot link: https://peerj.com/articles/6676 last-modified: 2019-04-09 description: BackgroundTiger beetles (Coleoptera: Cicindelidae) are predatory insects usually occurring in various sandy habitats. In south-eastern Europe, especially in lowland areas located close to the sea coast, the diversity of Cicindelidae is one of the highest in the Palaearctic realm. Although previous studies conducted in different areas of the world show that many species are habitat specialists, unfortunately little is known about environmental factors affecting the diversity and distribution of tiger beetles in this region.Material and MethodsHabitat preferences for 12 tiger beetles taxa were analysed. Over 100 samples collected in eight countries located in coastal areas of the Black and Mediterranean Seas were studied, for which climate data, macrohabitat types, and soil parameters (soil humidity, salinity, pH, and structure) were investigated.ResultsMost studied Cicindelidae were characterised by narrow or very narrow habitat specialisation and did not co-occur with other ones, including 11 taxa found as habitat specialists occurring only in one or two types of macrohabitat. The most eurythopic species was Calomera littoralis nemoralis which occupied four macrohabitat types. The climatic zone, altitude, and humidity were found as the most important factors in the distribution of the studied tiger beetle species. Salt marshes and sandy sea beaches were noted as the most diverse macrohabitat types.DiscussionTiger beetle fauna of south-eastern Europe consists mainly of habitat specialists sensitive to environmental changes, which makes these beetles perfect bioindicators. Moreover, as a great number of studied Cicindelidae taxa occur in habitats which are under a significant human impact, we suggest that in the studied area the group can be successfully used as a flagship taxon for insect and nature conservation. creator: Radomir Jaskuła creator: Mateusz Płóciennik creator: Axel Schwerk uri: https://doi.org/10.7717/peerj.6676 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Jaskuła et al. title: Aridity thresholds of soil microbial metabolic indices along a 3,200 km transect across arid and semi-arid regions in Northern China link: https://peerj.com/articles/6712 last-modified: 2019-04-09 description: Soil microbial processes are crucial for understanding the ecological functions of arid and semi-arid lands which occupy approximately 40% of the global terrestrial ecosystems. However, how soil microbial metabolic activities may change across a wide aridity gradient in drylands remains unclear. Here, we investigated three soil microbial metabolic indices (soil organic carbon (SOC)-based microbial respiration, metabolic quotient, and microbial biomass as a proportion of total SOC) and the degree of carbon limitation for microbial respiration along a 3,200 km transect with a wide aridity gradient. The aridity gradient was customarily expressed using the aridity index (AI) which was calculated as the ratio of mean annual precipitation to mean annual evaporation, therefore, a lower AI value indicated a higher degree of aridity. Our results showed non-linear relationships between AI values and the metabolic indices with a clear aridity threshold for each of the three metabolic indices along the aridity gradient, respectively (AI = 0.13 for basal respiration, AI = 0.17 for metabolic quotient, and AI = 0.17 for MBC:SOC ratio). These metabolic indices linearly declined when AI was above the thresholds, but did not show any clear patterns when AI was below the thresholds. We also found that soil microbial respiration was highly limited by available carbon substrates at locations with higher primary production and relatively lower level of water limitation when AI was above the threshold, a counter-intuitive pattern that microbes were more starved in ecosystems with more substrate input. However, the increasing level of carbon limitation did correspond to the declining trend of the three metabolic indices along the AI gradient, which indicates that the carbon limitation influences microbial metabolism. We also found that the ratio of microbial biomass carbon to SOC in arid regions (AI < 0.2) with extremely low precipitation and primary production were not quantitatively related to SOC content. Overall, our results imply that microbial metabolism is distinctively different in arid lands than in non-arid lands. creator: Jianfeng Hou creator: Feike A. Dijkstra creator: Xiuwei Zhang creator: Chao Wang creator: Xiaotao Lü creator: Peng Wang creator: Xingguo Han creator: Weixin Cheng uri: https://doi.org/10.7717/peerj.6712 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Hou et al. title: Throwing light on dark diversity of vascular plants in China: predicting the distribution of dark and threatened species under global climate change link: https://peerj.com/articles/6731 last-modified: 2019-04-09 description: BackgroundAs global climate change accelerates, ecologists and conservationists are increasingly investigating changes in biodiversity and predicting species distribution based on species observed at sites, but rarely consider those plant species that could potentially inhabit but are absent from these areas (i.e., the dark diversity and its distribution). Here, we estimated the dark diversity of vascular plants in China and picked up threatened dark species from the result, and applied maximum entropy (MaxEnt) model to project current and future distributions of those dark species in their potential regions (those regions that have these dark species).MethodsWe used the Beals probability index to estimate dark diversity in China based on available species distribution information and explored which environmental variables had significant impacts on dark diversity by incorporating bioclimatic data into the random forest (RF) model. We collected occurrence data of threatened dark species (Eucommia ulmoides, Liriodendron chinense, Phoebe bournei, Fagus longipetiolata, Amentotaxus argotaenia, and Cathaya argyrophylla) and related bioclimatic information that can be used to predict their distributions. In addition, we used MaxEnt modeling to project their distributions in suitable areas under future (2050 and 2070) climate change scenarios.ResultsWe found that every study region’s dark diversity was lower than its observed species richness. In these areas, their numbers of dark species are ranging from 0 to 215, with a generally increasing trend from western regions to the east. RF results showed that temperature variables had a more significant effect on dark diversity than those associated with precipitation. The results of MaxEnt modeling showed that most threatened dark species were climatically suitable in their potential regions from current to 2070.DiscussionsThe results of this study provide the first ever dark diversity patterns concentrated in China, even though it was estimated at the provincial scale. A combination of dark diversity and MaxEnt modeling is an effective way to shed light on the species that make up the dark diversity, such as projecting the distribution of specific dark species under global climate change. Besides, the combination of dark diversity and species distribution models (SDMs) may also be of value for ex situ conservation, ecological restoration, and species invasion prevention in the future. creator: Lili Tang creator: Runxi Wang creator: Kate S. He creator: Cong Shi creator: Tong Yang creator: Yaping Huang creator: Pufan Zheng creator: Fuchen Shi uri: https://doi.org/10.7717/peerj.6731 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Tang et al. title: Salivary LDOC1 is a gender-difference biomarker of oral squamous cell carcinoma link: https://peerj.com/articles/6732 last-modified: 2019-04-09 description: BackgroundThe X-linked tumor suppressor gene LDOC1 is reported to be involved in oral cancer. The detection of biomarkers in salivary RNA is a non-invasive strategy for diagnosing many diseases. The aim of the present study was to investigate the potential of salivary LDOC1 as a biomarker of oral cancer.MethodsWe determined the expression levels of LDOC1 in the saliva of oral squamous cell carcinoma (OSCC) subjects, and investigated its correlation with various clinicopathological characteristics. The expression levels of salivary LDOC1 were detected in 53 OSCC subjects and 43 healthy controls using quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis. We used Fisher’s exact test to analyze the correlations between expression levels and clinicopathological characteristics.ResultsSalivary LDOC1 was significantly upregulated in females with OSCC (p = 0.0072), and significantly downregulated in males with OSCC (p = 0.0206). Eighty-nine percent of male OSCC subjects who smoked expressed low levels of LDOC1. OSCC cell lines derived from male OSCC subjects expressed low levels of LDOC1.ConclusionsA high level of salivary LDOC1 expression is a biomarker of OSCC in females. A high percentage of male OSCC subjects who smoke express low levels of salivary LDOC1. A low level of salivary LDOC1 expression is a biomarker of OSCC in males. creator: Chung-Ji Liu creator: Jen-Hao Chen creator: Shih-Min Hsia creator: Chiu-Chu Liao creator: Hui-Wen Chang creator: Tzong-Ming Shieh creator: Yin-Hwa Shih uri: https://doi.org/10.7717/peerj.6732 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Distribution patterns of dinoflagellate communities along the Songhua River link: https://peerj.com/articles/6733 last-modified: 2019-04-09 description: BackgroundDinoflagellates have the potential to pose severe ecological and economic damages to aquatic ecosystems. It is therefore largely needed to understand the causes and consequences of distribution patterns of dinoflagellate communities in order to manage potential environmental problems. However, a majority of studies have focused on marine ecosystems, while the geographical distribution patterns of dinoflagellate communities and associated determinants in freshwater ecosystems remain unexplored, particularly in running water ecosystems such as rivers and streams.MethodsHere we utilized multiple linear regression analysis and combined information on species composition recovered by high-throughput sequencing and spatial and environmental variables to analyze the distribution patterns of dinoflagellate communities along the Songhua River.ResultsAfter high-throughput sequencing, a total of 490 operational taxonomic units (OTUs) were assigned to dinoflagellates, covering seven orders, 13 families and 22 genera. Although the sample sites were grouped into three distinctive clusters with significant difference (p < 0.05) in environmental variables, OTUs-based dinoflagellate communities among the three clusters showed no significant difference (p > 0.05). Among all 24 environmental factors, two environmental variables, including NO3-N and total dissolved solids (TDS), were selected as the significantly influential factors (p < 0.05) on the distribution patterns of dinoflagellate communities based on forward selection. The redundancy analysis (RDA) model showed that only a small proportion of community variation (6.1%) could be explained by both environmental (NO3-N and TDS) and dispersal predictors (watercourse distance) along the River. Variance partitioning revealed a larger contribution of local environmental factors (5.85%) than dispersal (0.50%) to the total variation of dinoflagellate communities.DiscussionOur findings indicated that in addition to the two quantifiable processes in this study (species sorting and dispersal), more unquantifiable stochastic processes such as temporal extinction and colonization events due to rainfall may be responsible for the observed geographical distribution of the dinoflagellate community along the Songhua River. Results obtained in this study suggested that deeper investigations covering different seasons are needed to understand the causes and consequences of geographical distribution patterns of dinoflagellate biodiversity in river ecosystems. creator: Yangchun Gao creator: Yiyong Chen creator: Wei Xiong creator: Shiguo Li creator: Aibin Zhan uri: https://doi.org/10.7717/peerj.6733 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Gao et al. title: Temporal variability in zooplankton community in the western Yellow Sea and its possible links to green tides link: https://peerj.com/articles/6641 last-modified: 2019-04-08 description: Large-scale macro-algal blooms of Ulva prolifera (also called green tides) have appeared each summer since 2008 in the western Yellow Sea. In this study, we investigated the temporal variability in zooplankton community in the western Yellow Sea and its possible links to green tides using data from a long-term plankton survey off the coast of Qingdao, China. Environmental conditions observed in the study area during the green tide period (GTP: June–August, 2008–2013) were compared to the non-green tide period (NGTP: June–August, 2005–2007), to support the contention that variations observed in zooplankton community may be attributed to the green tides, as opposed to natural climatic or environmental variations. Zooplankton assemblage structure observed during the GTP was then compared to the NGTP. Significant variations were detected both in zooplankton abundance and assemblage structure between the two defined periods. The abundance of zooplankton, mainly copepods, was significantly decreased during the GTP. Meanwhile, the relative abundance of copepods decreased by approximately 10% and that of gelatinous zooplankton, including appendicularians, chaetognaths, and medusae, almost doubled (ca. increased by 6.4%). The dominant species of meroplankton completely changed, specifically, polychaeta, and echinoderm larvae were more dominant than decapod and bivalve larvae. With regard to zooplankton size structure, the NGTP showed a higher size diversity with more small-sized organisms, while the GTP showed a lower size diversity in the community. According to general linear models, the interannual variation in summer zooplankton abundance was significantly correlated with green tides. These results indicate that the temporal changes in zooplankton community may have a close link to the green tides. creator: Weicheng Wang creator: Guangtao Zhang creator: Xiaoxia Sun creator: Fang Zhang creator: Xing Zhang uri: https://doi.org/10.7717/peerj.6641 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Wang et al.