Screening of prognostic biomarkers for endometrial carcinoma based on a ceRNA network
Objective This study aims to reveal the regulation network of lncRNAs-miRNAs-mRNA in endometrial carcinoma (EC), to investigate the underlying mechanisms of EC occurrence and progression, to screen prognostic biomarkers. Methods RNA-seq and miRNA-seq data of endometrial carcinoma were downloaded from the TCGA database. Edge.R package was used to screen differentially expressed genes. A database was searched to determine differentially expressed lncRNA-miRNA and miRNA-mRNA pairs, to construct the topological network of ceRNA, and to elucidate the key RNAs that are for a prognosis of survival. Results We screened out 2632 mRNAs, 1178 lncRNAs and 189 miRNAs that were differentially expressed. The constructed ceRNA network included 97 lncRNAs, 20 miRNAs and 73 mRNAs. Analyzing network genes for associations with prognosies revealed 169 prognosis-associated RNAs, including 92 lncRNAs, 16miRNAs and 61 mRNAs. Conclusion Our results reveal new potential mechanisms underlying the carcinogenesis and progression of endometrial carcinoma.
Zheng et al. (2018) Screening of prognostic biomarkers for endometrial carcinoma based on a ceRNA network. PeerJ 6:e6091 https://doi.org/10.7717/peerj.6091
The recent expansion of Fox Sparrow (Passerella iliaca iliaca) breeding range into the northeastern United States
The breeding range of the Eastern Fox Sparrow (Passerella iliaca iliaca) is generally recognized as comprising the boreal forest of Canada. However, recent observations suggest that the species is present during the summer months throughout much of the northeastern US, unexpected for a species characterized as a passage migrant in the region. To clarify, I conducted a literature review to document the historical status of the species in the northeastern US and then analyzed observations submitted to eBird to describe its recent and current status in the region. Historical accounts consistently identify Fox Sparrow as a passage migrant through the region during early spring and late fall. Beginning in the early 1980s, observers began noting regular extralimital records of Fox Sparrow in northern Maine. A single nest was discovered in the state in 1983, and another in northern New Hampshire in 1997. Despite the paucity of breeding records, observations submitted to eBird suggest that the southern limit of the breeding range of Fox Sparrow has expanded rapidly to the south and west in recent years. The proportion of complete checklists submitted to eBird that contained at least one observation of Fox Sparrow grew at an annual rate of 18% from 2003–2016 and was independent of observer effort. Fox Sparrow now occurs regularly on mountaintops and in young stands of spruce (Picea spp.) and balsam fir (Abies balsamea) during the breeding season throughout northern and western Maine and northern New Hampshire, with occasional records from the Green Mountains of Vermont and the Adirondack Mountains of New York. The cause of this rapid expansion of its breeding range is unknown, but may be related to an increase in the amount of young conifer forest in the northeastern US created by commercial timber harvest.
Lloyd (2018) The recent expansion of Fox Sparrow (Passerella iliaca iliaca) breeding range into the northeastern United States. PeerJ 6:e6087 https://doi.org/10.7717/peerj.6087
Posture similarity index: a method to compare hand postures in synergy space
Background The human hand can perform a range of manipulation tasks, from holding a pen to holding a hammer. The central nervous system (CNS) uses different strategies in different manipulation tasks based on task requirements. Attempts to compare postures of the hand have been made for use in robotics and animation industries. In this study, we developed an index called the posture similarity index to quantify the similarity between two human hand postures. Methods Twelve right-handed volunteers performed 70 postures, and lifted and held 30 objects (total of 100 different postures, each performed five times). A 16-sensor electromagnetic tracking system captured the kinematics of individual finger phalanges (segments). We modeled the hand as a 21-DoF system and computed the corresponding joint angles. We used principal component analysis to extract kinematic synergies from this 21-DoF data. We developed a posture similarity index (PSI), that represents the similarity between posture in the synergy (Principal component) space. First, we tested the performance of this index using a synthetic dataset. After confirming that it performs well with the synthetic dataset, we used it to analyze the experimental data. Further, we used PSI to identify postures that are “representative” in the sense that they have a greater overlap (in synergy space) with a large number of postures. Results Our results confirmed that PSI is a relatively accurate index of similarity in synergy space both with synthetic data and real experimental data. Also, more special postures than common postures were found among “representative” postures. Conclusion We developed an index for comparing posture similarity in synergy space and demonstrated its utility by using synthetic dataset and experimental dataset. Besides, we found that “special” postures are actually “special” in the sense that there are more of them in the “representative” postures as identified by our posture similarity index.
Bhatt et al. (2018) Posture similarity index: a method to compare hand postures in synergy space. PeerJ 6:e6078 https://doi.org/10.7717/peerj.6078
Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
Although microbes mediate much of the biogeochemical cycling in freshwater, the categories of carbon and nutrients currently used in models of freshwater biogeochemical cycling are too broad to be relevant on a microbial scale. One way to improve these models is to incorporate microbial data. Here, we analyze both genes and genomes from three metagenomic time series and propose specific roles for microbial taxa in freshwater biogeochemical cycles. Our metagenomic time series span multiple years and originate from a eutrophic lake (Lake Mendota) and a humic lake (Trout Bog Lake) with contrasting water chemistry. Our analysis highlights the role of polyamines in the nitrogen cycle, the diversity of diazotrophs between lake types, the balance of assimilatory vs. dissimilatory sulfate reduction in freshwater, the various associations between types of phototrophy and carbon fixation, and the density and diversity of glycoside hydrolases in freshwater microbes. We also investigated aspects of central metabolism such as hydrogen metabolism, oxidative phosphorylation, methylotrophy, and sugar degradation. Finally, by analyzing the dynamics over time in nitrogen fixation genes and Cyanobacteria genomes, we show that the potential for nitrogen fixation is linked to specific populations in Lake Mendota. This work represents an important step towards incorporating microbial data into ecosystem models and provides a better understanding of how microbes may participate in freshwater biogeochemical cycling.
Linz et al. (2018) Freshwater carbon and nutrient cycles revealed through reconstructed population genomes. PeerJ 6:e6075 https://doi.org/10.7717/peerj.6075
Technology-assisted white cane: evaluation and future directions
Background Several technology-assisted aids are available to help blind and visually impaired people perform their daily activities. The current research uses the state-of-the-art technology to enhance the utility of traditional navigational aids to produce solutions that are more reliable. In this regard, a white cane is no exception, which is supplemented with the existing technologies to design Electronic Travel Aids (ETAs), Electronic Orientation Aids (EOAs), and Position Locator Devices (PLDs). Although several review articles uncover the strengths and limitations of research contributions that extend traditional navigational aids, we find no review article that covers research contributions on a technology-assisted white cane. The authors attempt to fill this literature gap by reviewing the most relevant research articles published during 2010–2017 with the common objective of enhancing the utility of white cane with the existing technology. Methods The authors have collected the relevant literature published during 2010–17 by searching and browsing all the major digital libraries and publishers’ websites. The inclusion/exclusion criteria were applied to select the research articles that are relevant to the topic of this review article, and all other irrelevant papers were excluded. Among the 577 (534 through database searching and 43 through other sources) initially screened papers, the authors collected 228 full-text articles, which after applying exclusion/inclusion criteria resulted in 36 papers that were included in the evaluation, comparison, and discussion. This also includes research articles of commercially available aids published before the specified range. Results The findings show that the research trend is shifting towards developing a technology-assisted white cane solution that is applicable in both indoor and outdoor environments to aid blind users in navigation. In this regard, exploiting smartphones to develop low-cost and user-friendly navigation solution is among the best research opportunities to explore. In addition, the authors contribute a theoretical evaluation framework to compare and evaluate the state-of-the-art solutions, identify research trends and future directions. Discussion Researchers have been in the quest to find out ways of enhancing the utility of white cane using existing technology. However, for a more reliable enhancement, the design should have user-centric characteristics. It should be portable, reliable, trust-worthy, lightweight, less costly, less power hungry, and require minimal training with special emphasis on its ergonomics and social acceptance. Smartphones, which are the ubiquitous and general-purpose portable devices, should be considered to exploit its capabilities in making technology-assisted white cane smarter and reliable.
Khan et al. (2018) Technology-assisted white cane: evaluation and future directions. PeerJ 6:e6058 https://doi.org/10.7717/peerj.6058
The relationship between carbon and nitrogen metabolism in cucumber leaves acclimated to salt stress
The study examines the effect of acclimation on carbon and nitrogen metabolism in cucumber leaves subjected to moderate and severe NaCl stress. The levels of glucose, sucrose, NADH/NAD+-GDH, AspAT, AlaAT, NADP+-ICDH, G6PDH and 6GPDH activity were determined after 24 and 72 hour periods of salt stress in acclimated and non-acclimated plants. Although both groups of plants showed high Glc and Suc accumulation, they differed with regard to the range and time of accumulation. Acclimation to salinity decreased the activities of NADP+-ICDH and deaminating NAD+-GDH compared to controls; however, these enzymes, together with the other examined parameters, showed elevated values in the stressed plants. The acclimated plants showed higher G6PDH activity than the non-acclimated plants, whereas both groups demonstrated similar 6PGDH activity. The high activities of NADH-GDH, AlaAT and AspAT observed in the examined plants could be attributed to a high demand for glutamate. The observed changes may be required for the maintenance of correct TCA cycle activity, and acclimation appeared to positively influence these adaptive processes.
Environmental Contamination and Remediation
Naliwajski et al. (2018) The relationship between carbon and nitrogen metabolism in cucumber leaves acclimated to salt stress. PeerJ 6:e6043 https://doi.org/10.7717/peerj.6043
A direct approach to estimating false discovery rates conditional on covariates
Modern scientific studies from many diverse areas of research abound with multiple hypothesis testing concerns. The false discovery rate (FDR) is one of the most commonly used approaches for measuring and controlling error rates when performing multiple tests. Adaptive FDRs rely on an estimate of the proportion of null hypotheses among all the hypotheses being tested. This proportion is typically estimated once for each collection of hypotheses. Here, we propose a regression framework to estimate the proportion of null hypotheses conditional on observed covariates. This may then be used as a multiplication factor with the Benjamini–Hochberg adjusted p-values, leading to a plug-in FDR estimator. We apply our method to a genome-wise association meta-analysis for body mass index. In our framework, we are able to use the sample sizes for the individual genomic loci and the minor allele frequencies as covariates. We further evaluate our approach via a number of simulation scenarios. We provide an implementation of this novel method for estimating the proportion of null hypotheses in a regression framework as part of the Bioconductor package swfdr.
Boca et al. (2018) A direct approach to estimating false discovery rates conditional on covariates. PeerJ 6:e6035 https://doi.org/10.7717/peerj.6035
A new phylogenetic analysis of Phytosauria (Archosauria: Pseudosuchia) with the application of continuous and geometric morphometric character coding
Phytosauria is a clade of large, carnivorous, semi-aquatic archosauromorphs which reached its peak diversity and an almost global distribution in the Late Triassic (c. 230–201 Mya). Previous phylogenetic analyses of Phytosauria have either focused primarily on the relationships of specific subclades, or were limited in taxonomic scope, and no taxonomically comprehensive dataset is currently available. We here present the most taxonomically comprehensive cladistic dataset of phytosaurs to date, based on extensive first-hand study, identification of novel characters and synthesis of previous matrices. This results in an almost twofold increase in phylogenetic information scored per taxon over previous analyses. Alongside a traditional discrete character matrix, three variant matrices were analysed in which selected characters were coded using continuous and landmarking methods, to more rigorously explore phytosaur relationships. Based on these four data matrices, four tree topologies were recovered. Relationships among non-leptosuchomorph phytosaurs are largely consistent between these four topologies, whereas those of more derived taxa are more variable. Rutiodon carolinensis consistently forms a sister relationship with Angistorhinus. In three topologies Nicrosaurus nests deeply within a group of traditionally non-Mystriosuchini taxa, leading us to redefine Mystriosuchini by excluding Nicrosaurus as an internal specifier. Two distinct patterns of relationships within Mystriosuchini are present in the four topologies, distinguished largely by the variable position of Mystriosuchus. In two topologies Mystriosuchus forms the most basal clade in Mystriosuchini, whilst in the others it occupies a highly derived position within the Machaeroprosopus clade. ‘Redondasaurus’ is consistently recovered as monophyletic; however, it also nests within the Machaeroprosopus clade. The greatest impact on tree topology was associated with the incorporation of continuous data into our matrices, with landmark characters exerting a relatively modest influence. All topologies correlated significantly with stratigraphic range estimates. Topological variability in our results highlights clades in which further investigation may better elucidate phytosaur relationships.
Jones et al. (2018) A new phylogenetic analysis of Phytosauria (Archosauria: Pseudosuchia) with the application of continuous and geometric morphometric character coding. PeerJ 6:e5901 https://doi.org/10.7717/peerj.5901
Characterization and comparative genomic analysis of virulent and temperate Bacillus megaterium bacteriophages
Next-Generation Sequencing (NGS) technologies provide unique possibilities for the comprehensive assessment of the environmental diversity of bacteriophages. Several Bacillus bacteriophages have been isolated, but very few Bacillus megaterium bacteriophages have been characterized. In this study, we describe the biological characteristics, whole genome sequences, and annotations for two new isolates of the B. megaterium bacteriophages (BM5 and BM10), which were isolated from Egyptian soil samples. Growth analyses indicated that the phages BM5 and BM10 have a shorter latent period (25 and 30 min, respectively) and a smaller burst size (103 and 117 PFU, respectively), in comparison to what is typical for Bacillus phages. The genome sizes of the phages BM5 and BM10 were 165,031 bp and 165,213 bp, respectively, with modular organization. Bioinformatic analyses of these genomes enabled the assignment of putative functions to 97 and 65 putative ORFs, respectively. Comparative analysis of the BM5 and BM10 genome structures, in conjunction with other B. megaterium bacteriophages, revealed relatively high levels of sequence and organizational identity. Both genomic comparisons and phylogenetic analyses support the conclusion that the sequenced phages (BM5 and BM10) belong to different sub-clusters (L5 and L7, respectively), within the L-cluster, and display different lifestyles (lysogenic and lytic, respectively). Moreover, sequenced phages encode proteins associated with Bacillus pathogenesis. In addition, BM5 does not contain any tRNA sequences, whereas BM10 genome codes for 17 tRNAs.
Sharaf et al. (2018) Characterization and comparative genomic analysis of virulent and temperate Bacillus megaterium bacteriophages. PeerJ 6:e5687 https://doi.org/10.7717/peerj.5687
Enriched environment improves working memory impairment of mice with traumatic brain injury by enhancing histone acetylation in the prefrontal cortex
Working memory impairment is a common cognitive dysfunction after traumatic brain injury (TBI), which severely affects the quality of life of patients. Acetylcholine is a neurotransmitter which is closely related to cognitive functions. In addition, epigenetic modifications are also related to cognitive functions. A neurorehabilitation strategy, enriched environment (EE) intervention, has been widely used to improve cognitive impairment. However, studies of the mechanism of EE on cholinergic system and epigenetic modifications in mouse with TBI have not been reported yet. In this paper, a mouse model with traumatic frontal lobe injury was established, and the mechanism on EE for the mice with TBI was explored. It was found that EE could improve Y-maze performance of mice with TBI, the function of cholinergic system, and the imbalance of acetylation homeostasis in the prefrontal cortex of contralateral side of TBI. In addition, EE also could increase the level of CREB binding protein and histones H3 acetylation at ChAT gene promoter region in the prefrontal cortex of contralateral side of TBI. These indicate that EE has an important effect on the improvement of working memory impairment and the underlying mechanism may involve in histones H3 acetylation at ChAT gene promoter regions in the prefrontal cortex.
Wang et al. (2018) Enriched environment improves working memory impairment of mice with traumatic brain injury by enhancing histone acetylation in the prefrontal cortex. PeerJ 6:e6113 https://doi.org/10.7717/peerj.6113