Comprehensive circular RNA expression profile in radiation-treated HeLa cells and analysis of radioresistance-related circRNAs
Background Cervical cancer is one of the most common cancers in women worldwide. Malignant tumors develop resistance mechanisms and are less sensitive to or do not respond to irradiation. With the development of high-throughput sequencing technologies, circular RNA (circRNA) has been identified in an increasing number of diseases, especially cancers. It has been reported that circRNA can compete with microRNAs (miRNAs) to change the stability or translation of target RNAs, thus regulating gene expression at the transcriptional level. However, the role of circRNAs in cervical cancer and the radioresistance mechanisms of HeLa cells are unknown. The objective of this study is to investigate the role of circRNAs in radioresistance in HeLa cells. Methods High-throughput sequencing and bioinformatics analysis of irradiated and sham-irradiated HeLa cells. The reliability of high-throughput RNA sequencing was validated using quantitative real-time polymerase chain reaction. The most significant circRNA functions and pathways were selected by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. A circRNA–miRNA–target gene interaction network was used to find circRNAs associated with radioresistance. Moreover, a protein–protein interaction network was constructed to identify radioresistance-related hub proteins. Results High-throughput sequencing allowed the identification of 16,893 circRNAs involved in the response of HeLa cells to radiation. Compared with the control group, there were 153 differentially expressed circRNAs, of which 76 were up-regulated and 77 were down-regulated. GO covered three domains: biological process (BP), cellular component (CC) and molecular function (MF). The terms assigned to the BP domain were peptidyl-tyrosine dephosphorylation and regulation of cell migration. The identified CC terms were cell–cell adherens junction, nucleoplasm and cytosol, and the identified MF terms were protein binding and protein tyrosine phosphatase activity. The top five KEGG pathways were MAPK signaling pathway, endocytosis, axon guidance, neurotrophin signaling pathway, and SNARE interactions in vesicular transport. The protein–protein interaction analysis indicated that 19 proteins might be hub proteins. Conclusions CircRNAs may play a major role in the response to radiation. These findings may improve our understanding of the role of circRNAs in radioresistance in HeLa cells and allow the development of novel therapeutic approaches.
Yu et al. (2018) Comprehensive circular RNA expression profile in radiation-treated HeLa cells and analysis of radioresistance-related circRNAs. PeerJ 6:e5011 https://doi.org/10.7717/peerj.5011
Highly efficient removal of ammonia nitrogen from wastewater by dielectrophoresis-enhanced adsorption
A new approach, based on dielectrophoresis (DEP), was developed in this work to enhance traditional adsorption for the removal of ammonia nitrogen (NH3-N) from wastewater. The factors that affected the removal efficiency were systematically investigated, which allowed us to determine optimal operation parameters. With this new method we found that the removal efficiency was significantly improved from 66.7% by adsorption only to 95% by adsorption-DEP using titanium metal mesh as electrodes of the DEP and zeolite as the absorbent material. In addition, the dosage of the absorbent/zeolite and the processing time needed for the removal were greatly reduced after the introduction of DEP into the process. In addition, a very low discharge concentration (C, 1.5 mg/L) of NH3-N was achieved by the new method, which well met the discharge criterion of C < 8 mg/L (the emission standard of pollutants for rare earth industry in China).
Environmental Contamination and Remediation
Liu et al. (2018) Highly efficient removal of ammonia nitrogen from wastewater by dielectrophoresis-enhanced adsorption. PeerJ 6:e5001 https://doi.org/10.7717/peerj.5001
Drinking water and rural schools in the Western Amazon: an environmental intervention study
Background Although water and sanitation are considered human rights, worldwide approximately three of 10 people (2.1 billion) do not have access to safe drinking water. In 2016, 5.6 million students were enrolled in the 34% of Brazilian schools located in rural areas, but only 72% had a public water supply network. The objective was to evaluate effectiveness of environmental intervention for water treatment in rural schools of the Western Amazonia, and determine the efficacy of water treatment using a simplified chlorinator on potability standards for turbidity, fecal coliforms and Escherichia coli. Methods A simplified chlorinator was installed for treatment of potable water in 20 public schools in the rural area of Rio Branco municipality, Acre state, Brazil. Results Before the intervention, 20% (n = 4), 100% (n = 20) and 70% (n = 14) of schools had water that failed to meet potability standards for turbidity, fecal coliforms and E. coli, respectively. However, after intervention, 70% (p = 0.68), 75% (p < 0.001) and 100% (p < 0.001) of schools complied with potability standards. Discussion This intervention considerably improved schools’ water quality, thus decreasing children’s health vulnerability due to inadequate water. Ancillary activities including training, educational lectures, installation of equipment, supply of materials and supplies (65% calcium hypochlorite and reagents) were considered fundamental to achieving success full outcomes. Installation of a simplified chlorinator in rural schools of the Western Amazon is therefore proposed as a social technology aiming at social inclusion, as well as economic and environmental sustainability.
Ribeiro et al. (2018) Drinking water and rural schools in the Western Amazon: an environmental intervention study. PeerJ 6:e4993 https://doi.org/10.7717/peerj.4993
The use of chloroplast genome sequences to solve phylogenetic incongruences in Polystachya Hook (Orchidaceae Juss)
Background Current evidence suggests that for more robust estimates of species tree and divergence times, several unlinked genes are required. However, most phylogenetic trees for non-model organisms are based on single sequences or just a few regions, using traditional sequencing methods. Techniques for massive parallel sequencing or next generation sequencing (NGS) are an alternative to traditional methods that allow access to hundreds of DNA regions. Here we use this approach to resolve the phylogenetic incongruence found in Polystachya Hook. (Orchidaceae), a genus that stands out due to several interesting aspects, including cytological (polyploid and diploid species), evolutionary (reticulate evolution) and biogeographical (species widely distributed in the tropics and high endemism in Brazil). The genus has a notoriously complicated taxonomy, with several sections that are widely used but probably not monophyletic. Methods We generated the complete plastid genome of 40 individuals from one clade within the genus. The method consisted in construction of genomic libraries, hybridization to RNA probes designed from available sequences of a related species, and subsequent sequencing of the product. We also tested how well a smaller sample of the plastid genome would perform in phylogenetic inference in two ways: by duplicating a fast region and analyzing multiple copies of this dataset, and by sampling without replacement from all non-coding regions in our alignment. We further examined the phylogenetic implications of non-coding sequences that appear to have undergone hairpin inversions (reverse complemented sequences associated with small loops). Results We retrieved 131,214 bp, including coding and non-coding regions of the plastid genome. The phylogeny was able to fully resolve the relationships among all species in the targeted clade with high support values. The first divergent species are represented by African accessions and the most recent ones are among Neotropical species. Discussion Our results indicate that using the entire plastid genome is a better option than screening highly variable markers, especially when the expected tree is likely to contain many short branches. The phylogeny inferred is consistent with the proposed origin of the genus, showing a probable origin in Africa, with later dispersal into the Neotropics, as evidenced by a clade containing all Neotropical individuals. The multiple positions of Polystachya concreta (Jacq.) Garay & Sweet in the phylogeny are explained by allotetraploidy. Polystachya estrellensis Rchb.f. can be considered a genetically distinct species from P. concreta and P. foliosa (Lindl.) Rchb.f., but the delimitation of P. concreta remains uncertain. Our study shows that NGS provides a powerful tool for inferring relationships at low taxonomic levels, even in taxonomically challenging groups with short branches and intricate morphology.
Abreu et al. (2018) The use of chloroplast genome sequences to solve phylogenetic incongruences in Polystachya Hook (Orchidaceae Juss). PeerJ 6:e4916 https://doi.org/10.7717/peerj.4916
Is right coronary artery chronic total vessel occlusion impacting the surgical revascularization results of patients with multivessel disease? A retrospective study
Introduction Chronic total occlusion (CTO) is common in the presence of other significantly narrowed coronary arteries. The impact of total occlusion and its association with completeness of revascularization on patients with multivessel disease undergoing coronary artery bypass graft (CABG) remains largely unknown. Aim The aim of our study was to compare CABG operation characteristics, as well as 30-day mortality, incidence of post-operative major adverse cardiac and cerebrovascular events (MACCE) between patients with and without CTO in right coronary artery (RCA). Materials and Methods A total of 156 consecutive patients were included in the analysis. CTO of RCA or right posterior descending artery (RPD) was diagnosed in 57 patients (CTO-RCA group). Coronary stenosis without CTO in RCA was diagnosed in 99 patients (nonCTO-RCA group). Baseline characteristics were comparable in both groups. Results The majority of patients had class II (49.1% vs. 46%, p = 0.86) or class III (42.1% vs. 43%, p = 1.0) Canadian Cardiovascular Society grading system symptoms. Patients in the CTO-RCA group had in average 2.2 grafts implanted, as opposed to 2.4 grafts in patients in the nonCTO-RCA group (p = 0.003). Graft to the RCA was performed in 40.3% patients in the CTO-RCA group and in 81% patients in the nonCTO-RCA group (p = 0.001). The 30-day mortality from any cause or cardiac cause did not differ between groups (7% vs. 2%, p = 0.14 and 3.5% vs. 2%, p = 0.57 respectively). In a multivariate analysis CTO in RCA or RPD and peripheral artery disease were independent predictors of post-operative MACCE (7.9 (1.434–43.045) p = 0.02; 18.8 (3.451–101.833) p < 0.01, respectively). Conclusions Chronic total occlusion of RCA was found to be associated with smaller number of grafts performed during the CABG procedure. Although mortality between patients in the CTO-RCA and nonCTO-RCA groups did not differ, patients in the CTO-RCA group had higher incidence of post-operative MACCE.
Konstanty-Kalandyk et al. (2018) Is right coronary artery chronic total vessel occlusion impacting the surgical revascularization results of patients with multivessel disease? A retrospective study. PeerJ 6:e4909 https://doi.org/10.7717/peerj.4909
The effect of recent competition between the native Anolis oculatus and the invasive A. cristatellus on display behavior
Invasive species are a global threat to biodiversity. Cases where the invasion has been tracked since its beginning are rare, however, such that the first interactions between invasive and native species remain poorly understood. Communication behavior is an integral part of species identity and is subject to selection. Consequently, resource use and direct interference competition between native and invasive species may drive its evolution. Here, we tested the role of interactions between the recently introduced invasive lizard Anolis cristatellus and the native Anolis oculatus on variation in behavior and communication in Calibishie (Dominica). From May to June 2016, we filmed 122 adult males of both species displaying in banana farms under two contexts (allopatry and sympatry). We then recorded (i) the proportion of time spent displaying and (ii) the relative frequency of dewlap vs. push-up displays. To control for habitat variation, we measured and compared the habitat characteristics (canopy openness and habitat openness) of 228 males in allopatry and sympatry. While the habitat characteristics and total display-time did not differ between the contexts for the two species, the proportion of display-time spent dewlapping by A. cristatellus decreased in sympatry. The display of A. oculatus did not differ between the contexts, however. Shifts in microhabitat use, predation pressure, or interspecific interference are potential factors which might explain the behavioral changes in display observed in A. cristatellus. This study highlights the role of behavioral traits as a first response of an invasive species to recent competition with a closely related native species.
Dufour et al. (2018) The effect of recent competition between the native Anolis oculatus and the invasive A. cristatellus on display behavior. PeerJ 6:e4888 https://doi.org/10.7717/peerj.4888
A new minute ectosymbiotic harpacticoid copepod living on the sea cucumber Eupentacta fraudatrix in the East/Japan Sea
The ectosymbiotic copepods, Vostoklaophonte eupenta gen. & sp. nov. associated with the sea cucumber Eupentacta fraudatrix, was found in the subtidal zone of Peter the Great Bay, East/Japan Sea. The new genus, Vostoklaophonte, is similar to Microchelonia in the flattened body form, reduced mandible, maxillule and maxilla, but with well-developed prehensile maxilliped, and in the reduced segmentation and setation of legs 1–5. Most appendages of the new genus are more primitive than those of Microchelonia. The inclusion of the symbiotic genera Microchelonia and Vostoklaophonte gen. nov. in Laophontidae, as well as their close phylogenetic relationships, are supported by morphological observations and molecular data. This is the third record of laophontid harpacticoid copepods living in symbiosis with sea cucumbers recorded from the Korean and Californian coasts.
Yeom et al. (2018) A new minute ectosymbiotic harpacticoid copepod living on the sea cucumber Eupentacta fraudatrix in the East/Japan Sea. PeerJ 6:e4979 https://doi.org/10.7717/peerj.4979
Reproductive ecology of the endangered Beal’s-eyed turtle, Sacalia bealei
The Beal’s-eyed turtle (Sacalia bealei) is endemic to southeastern China and endangered due to poaching and habitat loss. Knowledge of S. bealei ecology is lacking and this study provides baseline information of its reproduction in a natural environment. We studied the reproductive ecology of S. bealei using X-ray, spool-and-line tracking, and direct observation. Six nesting females were successfully tracked and their nesting behaviors are documented in detail. Females produced a mean clutch size of 2.2 eggs (range 1–3). The hard-shelled eggs were ellipsoidal with a mean length of 45.50 mm, a mean width of 23.20 mm, and mean weight of 14.8 g. The relative clutch mass was 9.47%, while the relative egg mass was 4.60%. The mean incubation period was 94.7 days with a mean nest temperature of 25.08 °C. Hatchlings had a mean weight of 9.7 g, carapace length of 40.1 mm, carapace width of 33.3 mm, carapace height of 17.4 mm, plastron length of 31.6 mm, and plastron width of 25.4 mm. The results of this study provide important information to inform conservation plans and ex-situ breeding for this endangered species.
Lin et al. (2018) Reproductive ecology of the endangered Beal’s-eyed turtle, Sacalia bealei. PeerJ 6:e4997 https://doi.org/10.7717/peerj.4997
Structural insights and characterization of human Npas4 protein
Npas4 is an activity dependent transcription factor which is responsible for gearing the expression of target genes involved in neuro-transmission. Despite the importance of Npas4 in many neuronal diseases, the tertiary structure of Npas4 protein along with its physico-chemical properties is limited. In the current study, first we perfomed the phylogenetic analysis of Npas4 and determined the content of hydrophobic, flexible and order-disorder promoting amino acids. The protein binding regions, post-translational modifications and crystallization propensity of Npas4 were predicted through different in-silico methods. The three dimensional model of Npas4 was predicted through LOMET, SPARSKS-X, I-Tasser, RaptorX, MUSTER and Pyhre and the best model was selected on the basis of Ramachandran plot, PROSA, and Qmean scores. The best model was then subjected to further refinement though MODREFINER. Finally the interacting partners of Npas4 were identified through STRING database. The phylogenetic analysis showed the human Npas4 gene to be closely related to other primates such as chimpanzees, monkey, gibbon. The physiochemical properties of Npas4 showed that it is an intrinsically disordered protein with N-terminal ordered region. The post-translational modification analyses indicated absence of acetylation and mannosylation sites. Three potential phosphorylation sites (S108, T130 and T136) were found in PAS A domain whilst a single phosphorylation site (S273) was present in PAS B domain. The predicted tertiary structure of Npas4 showed that bHLH domain and PAS domain possess tertiary structures while the rest of the protein exhibited disorder property. Protein-protein interaction analysis revealed NPas4 interaction with various proteins which are mainly involved in nuclear trafficking of proteins to cytoplasm, activity regulated gene transcription and neurodevelopmental disorders. Moreover the analysis also highlighted the direct relation to proteins involved in promoting neuronal survival, plasticity and cAMP responsive element binding protein proteins. The current study helps in understanding the physicochemical properties and reveals the neuro-modulatory role of Npas4 in crucial pathways involved in neuronal survival and neural signalling hemostasis.
Fahim et al. (2018) Structural insights and characterization of human Npas4 protein. PeerJ 6:e4978 https://doi.org/10.7717/peerj.4978
Histology of 24 organs from Asian elephant calves (Elephas maximus)
Background Elephants are the largest and heaviest living terrestrial animals, but information on their histology is still lacking. This study provides a unique insight into the elephant’s organs and also provides a comparison between juvenile Asian elephants and adult Asian elephants or other species. Here we report on the histological structure of 24 organs, including the skin, brain (cerebrum, cerebellar hemisphere, vermis, thalamus, midbrain), spinal cord, sciatic nerve, striated skeletal muscle, cardiac muscle, bone (flat bone and long bone), cartilage (hyaline cartilage and fibrocartilage), heart (right atrium, right ventricle), blood vessels (aorta, pulmonary artery and caudal vena cava), trunk, trachea, lung, tongue, esophagus, stomach, small intestine (duodenum, jejunum, ileum), large intestine (cecum, colon, rectum), liver and pancreas, kidney, ovary, uterus (body and horn) and spleen of two juvenile Asian elephants. Methods Tissue sections were stained with Harris’s hematoxylin and eosin Y. Results While almost all structures were similar to those of other species or adult elephants, some structures were different from other mammalian species, such as: plexiform bone was found in flat bone only; a thin trachealismuscle was observed in the trachea; and no serous or mucinous glands were found in the submucosa of the trachea. Discussion Histological information from various organs can serve as an important foundation of basal data for future microanatomical studies, and help in the diagnosis and pathogenesis in sick elephants or those with an unknown cause of death.
Thitaram et al. (2018) Histology of 24 organs from Asian elephant calves (Elephas maximus). PeerJ 6:e4947 https://doi.org/10.7717/peerj.4947