Metabolomic analysis reveals the mechanism of aluminum cytotoxicity in HT-29 cells
Background Aluminum (Al) is toxic to animals and humans. The most common sources of human exposure to Al are food and beverages. The intestinal epithelium is the first barrier against Al-induced toxicity. In this study, HT-29, a human colon cancer cell line, was selected as an in vitro model to evaluate the Al-induced alteration in metabolomic profiles and explore the possible mechanisms of Al toxicity. Methods MTT assay was performed to determine the half-maximal inhibitory concentration of Al ions. Liquid chromatography-mass spectrometry (LC-MS) was used for metabolomic analysis, and its results were further confirmed using quantitative reverse transcription polymerase chain reaction (RT-qPCR) of nine selected genes. Results Al inhibited the growth of the HT-29 cells, and its half-maximal dose for the inhibition of cell proliferation was found to be four mM. This dose was selected for further metabolomic analysis, which revealed that 81 metabolites, such glutathione (GSH), phosphatidylcholines, phosphatidylethanolamines, and creatine, and 17 metabolic pathways, such as the tricarboxylic acid cycle, pyruvate metabolism, and GSH metabolism, were significantly altered after Al exposure. The RT-qPCR results further confirmed these findings. Conclusion The metabolomics and RT-qPCR results indicate that the mechanisms of Al-induced cytotoxicity in HT-29 cells include cellular apoptosis, oxidative stress, and alteration of lipid, energy, and amino acid metabolism.
Yu et al. (2019) Metabolomic analysis reveals the mechanism of aluminum cytotoxicity in HT-29 cells. PeerJ 7:e7524 https://doi.org/10.7717/peerj.7524
Determination of nucleotide and enzyme degradation in haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) after high pressure processing
Background The degradation of nucleotides and their enzymes had been widely used to evaluate fish freshness. Immediately after fish death, adenosine triphosphate (ATP) degrades into inosine-5-monophosphate (IMP) via adenosine-5-diphosphate (ADP) and adenosine-5-monophosphate (AMP). IMP degradation continues to produce inosine (ino) and hypoxanthine (Hx) and further deteriorates the fish by producing xanthine and uric acid. The dephosphorylation of IMP to Ino is carried out by the enzyme 5′-nucleotidase (5′-NT), whereas the degradation of Ino to Hx is carried out by the enzyme nucleoside phosphorylase (NP). This study assesses the application of high pressure processing (HPP) in two species of fishes; haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) as a means to extend the shelf-life by slowing down the rate of nucleotides degradation. Methods Haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) fillets were subjected to HPP at 200, 250 and 300 MPa for 1 and 3 min before being stored for 14 days. In addition, 5′-NT and NP enzyme activities were determined on both fish species that were subjected to 100–600 MPa for 1 and 3 min. Results Adenosine triphosphate, ADP and AMP in both haddock and herring were lower at higher pressure levels. Inosine (Ino) increased (p < 0.05) after treatment at higher pressures in both species. Hx in herring decreased significantly (p < 0.05) at higher pressures but not in haddock. K values are the ratio of Ino and Hx to all nucleotides. K values in haddock were not significantly (p > 0.05) affected by the pressure treatment. H values are ratio of Hx to the sum of IMP, Ino and Hx. H values in haddock were significantly decreased (p < 0.05) with increasing pressure level. F values are ratio of IMP to the sum of IMP, Ino and Hx. F values showed no significant effects (p > 0.05) after pressure treatment. Furthermore, K values in control herring were significantly higher (p < 0.05) than those of the pressure-treated samples. H values in herring decreased significantly (p < 0.05) with increasing pressure level. F values in herring showed no significant effects (p > 0.05) after pressure treatment. Pressure treatment brought a significant decrease (p < 0.05) in protein content in both haddock and herring. 5′-NT activity was 20–35 fold higher compared to NP activity in haddock and 15–44 fold higher than NP activity in herring. 5′-NT and NP activities decreased significantly with increasing pressure level in both species. Discussion High pressure processing effectively slows down the conversion of Ino to Hx, delaying the undesirable flavour that develops in spoiling fish. The autolytic conversion of IMP to Ino by endogenous 5′-NT predominates in the earliest stages of storage is an autolytic process. However, both bacterial and endogenous NP enzymes are probably responsible for the gradual accumulation of Hx in fish. K values are recommended as a useful measurement of fish freshness.
Karim et al. (2019) Determination of nucleotide and enzyme degradation in haddock (Melanogrammus aeglefinus) and herring (Clupea harengus) after high pressure processing. PeerJ 7:e7527 https://doi.org/10.7717/peerj.7527
Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus)
Arthropods often have obligate relationships with symbiotic microbes, and recent investigations have demonstrated that such host-microbe relationships could be exploited to suppress natural populations of vector carrying mosquitos. Strategies that target the interplay between agricultural pests and their symbionts could decrease the burden caused by agricultural pests; however, the lack of comprehensive genomic insights into naturally occurring microbial symbionts presents a significant bottleneck. Here we employed amplicon surveys, genome-resolved metagenomics, and scanning electron microscopy to investigate symbionts of the wheat stem sawfly (Cephus cinctus), a major pest that causes an estimated $350 million dollars or more in wheat yield losses in the northwestern United States annually. Through 16S rRNA gene sequencing of two major haplotypes and life stages of wheat stem sawfly, we show a novel Spiroplasma species is ever-present and predominant, with phylogenomic analyses placing it as a member of the ixodetis clade of mollicutes. Using state-of-the-art metagenomic assembly and binning strategies we were able to reconstruct a 714 Kb, 72.7%-complete Spiroplasma genome, which represents just the second draft genome from the ixodetis clade of mollicutes. Functional annotation of the Spiroplasma genome indicated carbohydrate-metabolism involved PTS-mediated import of glucose and fructose followed by glycolysis to lactate, acetate, and propionoate. The bacterium also encoded biosynthetic pathways for essential vitamins B2, B3, and B9. We identified putative Spiroplasma virulence genes: cardiolipin and chitinase. These results identify a previously undescribed symbiosis between wheat stem sawfly and a novel Spiroplasma sp., availing insight into their molecular relationship, and may yield new opportunities for microbially-mediated pest control strategies.
Yeoman et al. (2019) Genome-resolved insights into a novel Spiroplasma symbiont of the Wheat Stem Sawfly (Cephus cinctus). PeerJ 7:e7548 https://doi.org/10.7717/peerj.7548
Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron (Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum
This study aimed to investigate the effects of Clostridium butyricum as a dietary probiotic supplement in fishmeal based diet on growth, gut microbiota and immune performance of marron (Cherax cainii). Marron were randomly distributed into two different treatment groups, control and probiotic fed group. After 42 days of feeding trial, the results revealed a significant (P < 0.05) increase in growth due to increase in number of moults in marron fed probiotics. The probiotic diet also significantly enhanced the total haemocyte counts (THC), lysozyme activity in the haemolymph and protein content of the tail muscle in marron. Compared to control, the 16S rRNA sequences data demonstrated an enrichment of bacterial diversity in the probiotic fed marron where significant increase of Clostridium abundance was observed. The abundance for crayfish pathogen Vibrio and Aeromonas were found to be significantly reduced post feeding with probiotic diet. Predicted metabolic pathway revealed an increased activity for the metabolism and absorption of carbohydrate, degradation of amino acid, fatty acid and toxic compounds, and biosynthesis of secondary metabolites. C. butyricum supplementation also significantly modulated the expression level of immune-responsive genes of marron post challenged with Vibrio mimicus. The overall results suggest that C. butyricum could be used as dietary probiotic supplement in marron aquaculture.
Foysal et al. (2019) Marked variations in gut microbiota and some innate immune responses of fresh water crayfish, marron (Cherax cainii, Austin 2002) fed dietary supplementation of Clostridium butyricum. PeerJ 7:e7553 https://doi.org/10.7717/peerj.7553
Prevalence of near-death experiences in people with and without REM sleep intrusion
Background The origin and prevalence of near-death experiences are unknown. A recent study suggested a link with REM sleep intrusion but was criticized for its selection of control participants. We therefore assessed the association of REM intrusion and near-death experiences with different methods. Methods Using a crowd-sourcing platform, we recruited 1,034 lay people from 35 countries to investigate the prevalence of near-death experiences and self-reported REM sleep intrusion. Reports were validated using the Greyson Near-Death Experiences Scale (GNDES) with ≥7 points as cut-off for near-death experiences. Results Near-death experiences were reported by 106 of 1,034 participants (10%; 95% CI [8.5–12%]). Evidence of REM intrusion was more common in people with near-death experiences (n = 50∕106; 47%) than in people with experiences with 6 points or less on the GNDES (n = 47∕183; 26%) or in those without such experiences (n = 107∕744; 14%; p = < 0.0001). Following multivariate regression analysis to adjust for age, gender, place of residence, employment and perceived danger, this association remained highly significant; people with REM intrusion were more likely to exhibit near-death experiences than those without (OR 2.85; 95% CI [1.68–4.88]; p = 0.0001). Discussion Using a crowd-sourcing approach, we found a prevalence of near-death experiences of 10%. While age, gender, place of residence, employment status and perceived threat do not seem to influence the prevalence of near-death experiences, we confirmed a possible association with REM sleep intrusion.
Kondziella et al. (2019) Prevalence of near-death experiences in people with and without REM sleep intrusion. PeerJ 7:e7585 https://doi.org/10.7717/peerj.7585
Insights from the proteome profile of Phytophthora capsici in response to the novel fungicide SYP-14288
Phytophthora capsica is a destructive oomycete plant pathogen that causes huge losses to crop production worldwide. However, the novel fungicide SYP-14288 has shown excellent activity against various stages of the oomycete life cycle as well against fungal plant pathogens. The current study utilized isobaric tags for relative and absolute quantitation technology to generate proteome profiles of P. capsici in the presence or absence of SYP-14288 in order to gain a greater understanding of the SYP-14288 mode of action. A total of 1,443 individual proteins were identified during the investigation, of which 599 were considered to have significantly altered expression. Further investigation using Cluster of Orthologous Groups of proteins analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated most of the proteins with altered expression were associated with carbohydrate metabolism, energy metabolism and their downstream biological functions, especially with regard to oxidoreductase activity and subsequent adenosine triphosphate (ATP) production associated pathways. Quantitative expression analysis using qRT-PCR validated the proteomic data. These results seem to indicate that SYP-14288 treatment caused a shift in energy metabolism that resulted in the activation of compensatory mechanisms affecting carbohydrate and lipid metabolism. The study also found evidence that the up-regulation of transmembrane transporters and proteins associated with stress response might also be coopted to compensate for the disrupted proton gradient and other downstream effects. Taken together these results provide strong evidence that SYP-14288 has a similar mode of action to the oxidative phosphorylation uncoupler Fluazinam but further investigation, including molecular studies, is required to completely characterize the SYP-14288 mode of action in P. capsici. However, the proteomic data collected in the current study does provide important insight into the overall effect of SYP-14288 in P. capsici, which could be useful for the registration and application of this novel fungicide.
Cai et al. (2019) Insights from the proteome profile of Phytophthora capsici in response to the novel fungicide SYP-14288. PeerJ 7:e7626 https://doi.org/10.7717/peerj.7626
Filter feeding in Late Jurassic pterosaurs supported by coprolite contents
Diets of pterosaurs have mainly been inferred from indirect evidence such as comparative anatomy, associations of co-occurring fossils, and functional morphology. Gut contents are rare, and until now there is only a single coprolite (fossil dropping), with unidentified inclusions, known. Here we describe three coprolites collected from a palaeosurface with numerous pterosaur tracks found in early Kimmeridgian (Hypselocyclum Zone) intertidal deposits of the Wierzbica Quarry, Poland. The specimens’ morphology and association to the tracks suggest a pterosaur producer. Synchrotron scans reveal numerous small inclusions, with foraminifera making up the majority of the identifiable ones. Other small remains include shells/carapaces (of bivalves, ostracods, and other crustaceans/arthropods) and bristles (some possibly of polychaete worms). The high density of the small shelly inclusions suggest that they were not accidently ingested, but constituted an important food source for the pterosaur(s), perhaps together with unpreserved soft-bodied animals. The combined evidence from the tracks and coprolites suggest a filter-feeding ctenochasmatid as the most likely tracemaker. If true, this significantly expands the bromalite record for this pterosaur group, which was previously only known from gastroliths. Moreover, this study also provides the first direct evidence of filter feeding in Jurassic pterosaurs and shows that they had a similar diet to the recent Chilean flamingo (Phoenicopterus chilensis).
Qvarnström et al. (2019) Filter feeding in Late Jurassic pterosaurs supported by coprolite contents. PeerJ 7:e7375 https://doi.org/10.7717/peerj.7375
The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations
Background The RIPper (http://theripper.hawk.rocks) is a set of web-based tools designed for analyses of Repeat-Induced Point (RIP) mutations in the genome sequences of Ascomycota. The RIP pathway is a fungal genome defense mechanism that is aimed at identifying repeated and duplicated motifs, into which it then introduces cytosine to thymine transition mutations. RIP thus serves to deactivate and counteract the deleterious consequences of selfish or mobile DNA elements in fungal genomes. The occurrence, genetic context and frequency of RIP mutations are widely used to assess the activity of this pathway in genomic regions of interest. Here, we present a bioinformatics tool that is specifically fashioned to automate the investigation of changes in RIP product and substrate nucleotide frequencies in fungal genomes. Results We demonstrated the ability of The RIPper to detect the occurrence and extent of RIP mutations in known RIP affected sequences. Specifically, a sliding window approach was used to perform genome-wide RIP analysis on the genome assembly of Neurospora crassa. Additionally, fine-scale analysis with The RIPper showed that gene regions and transposable element sequences, previously determined to be affected by RIP, were indeed characterized by high frequencies of RIP mutations. Data generated using this software further showed that large proportions of the N. crassa genome constitutes RIP mutations with extensively affected regions displaying reduced GC content. The RIPper was further useful for investigating and visualizing changes in RIP mutations across the length of sequences of interest, allowing for fine-scale analyses. Conclusion This software identified RIP targeted genomic regions and provided RIP statistics for an entire genome assembly, including the genomic proportion affected by RIP. Here, we present The RIPper as an efficient tool for genome-wide RIP analyses.
van Wyk et al. (2019) The RIPper, a web-based tool for genome-wide quantification of Repeat-Induced Point (RIP) mutations. PeerJ 7:e7447 https://doi.org/10.7717/peerj.7447
Profiling the lncRNA-miRNA-mRNA ceRNA network to reveal potential crosstalk between inflammatory bowel disease and colorectal cancer
Background Because of the increasing dysplasia rate in the lifelong course of inflammatory bowel disease (IBD) patients, it is imperative to characterize the crosstalk between IBD and colorectal cancer (CRC). However, there have been no reports revealing the occurrence of the ceRNA network in IBD-related CRC. Methods In this study, we conducted gene expression profile studies of databases and performed an integrated analysis to detect the potential of lncRNA-miRNA-mRNA ceRNA in regulating disease transformation. R packages were used to screen differentially expressed mRNA, lncRNA and miRNA among CRC, IBD and normal tissue. The lncRNA-miRNA-mRNA network was constructed based on predicted miRNA-targeted lncRNAs and miRNA-targeted mRNAs. Functional analyses were then conducted to identify genes involved in the ceRNA network, and key lncRNAs were evaluated based on several clinical outcomes. Results A total of three lncRNAs, 15 miRNAs, and 138 mRNAs were identified as potential mediators in the pathophysiological processes of IBD-related CRC. Gene Ontology annotation enrichment analysis confirmed that the dysplasia process was strongly associated with immune response, response to lipopolysaccharide, and inflammatory response. Survival analysis showed that LINC01106 (HR = 1.7; p < 0.05) were strongly associated with overall survival of colorectal cancer patients. The current study identified a series of IBD-related mRNAs, miRNA, and lncRNAs, and highlighted the important role of ceRNAs in the pathogenesis of IBD-related CRC. Among them, the LINC01106-miRNA-mRNA axis was identified as vital targets for further research.
Sun et al. (2019) Profiling the lncRNA-miRNA-mRNA ceRNA network to reveal potential crosstalk between inflammatory bowel disease and colorectal cancer. PeerJ 7:e7451 https://doi.org/10.7717/peerj.7451
Effectiveness of small road tunnels and fences in reducing amphibian roadkill and barrier effects at retrofitted roads in Sweden
Schemes to reduce road impacts on amphibians have been implemented for decades in Europe, yet, several aspects on the effectiveness of such schemes remain poorly understood. Particularly in northern Europe, including Sweden, there is a lack of available information on road mitigation for amphibians, which is hampering implementation progress and cost-effectiveness analyses of mitigation options. Here, we present data derived from systematic counts of amphibians during spring migration at three previous hot-spots for amphibian roadkill in Sweden, where amphibian tunnels with guiding fences have been installed. We used the data in combination with a risk model to estimate the number of roadkills and successful crossings before vs. after mitigation and mitigated vs. adjacent non-mitigated road sections. In mitigated road sections, the estimated number of amphibians killed or at risk of being killed by car traffic decreased by 85–100% and the estimated number successfully crossing the road increased by 25–340%. Data, however, suggested fence-end effects that may moderate the reduction in roadkill. We discuss possible explanations for the observed differences between sites and construction types, and implications for amphibian conservation. We show how effectiveness estimates can be used for prioritizing amphibian passages along the existing road network. Finally, we emphasize the importance of careful monitoring of amphibian roadkill and successful crossings before and after amphibian passages are constructed.
Helldin et al. (2019) Effectiveness of small road tunnels and fences in reducing amphibian roadkill and barrier effects at retrofitted roads in Sweden. PeerJ 7:e7518 https://doi.org/10.7717/peerj.7518