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
Detecting the impact of land cover change on observed rainfall
Analysis of observational data to pinpoint impact of land cover change on local rainfall is difficult due to multiple environmental factors that cannot be strictly controlled. In this study we use a statistical approach to identify the relationship between removal of tree cover and rainfall with data from best available sources for two large areas in Australia. Gridded rainfall data between 1979 and 2015 was used for the areas, while large scale (exogenous) effects were represented by mean rainfall across a much larger area and climatic indicators, such as Southern Oscillation Index and Indian Ocean Dipole. Both generalised additive modelling and step trend tests were used for the analysis. For a region in south central Queensland, the reported change in tree clearing between 2002–2005 did not result in strong statistically significant precipitation changes. On the other hand, results from a bushfire affected region on the border of New South Wales and Victoria suggest significant changes in the rainfall due to changes in tree cover. This indicates the method works better when an abrupt change in the data can be clearly identified. The results from the step trend test also mainly identified a positive relationship between the tree cover and the rainfall at p < 0.1 at the NSW/Victoria region. High rainfall variability and possible regrowth could have impacted the results in the Queensland region.
Liang et al. (2019) Detecting the impact of land cover change on observed rainfall. PeerJ 7:e7523 https://doi.org/10.7717/peerj.7523
Three new species, one new genus and subfamily of Dorylaimida (de Man, 1876) Pearse, 1942, and revisions on the families Tylencholaimellidae Jairajpuri, 1964 and Mydonomidae Thorne, 1964 (Nematoda: Dorylaimida)
Three new species of the order Dorylaimida (de Man, 1876) Pearse, 1942 were identified and described. Paratylencholaimus sanshaensis gen. nov. sp. nov. from Hainan is proposed as a new member of the family Tylencholaimellidae Jairajpuri, 1964. Paratylencholaimus gen. nov. is close to Phellonema Thorne, 1964 and Goferus Jairajpuri & Ahmad, 1992 but can be differentiated mainly by having basal part of odontophore rod-like and without knobs, and basal part of pharynx expanded gradually. Tylencholaimus zhongshanensis sp. nov. from Guangdong and Dorylaimoides shapotouensis sp. nov. from the Ningxia Hui Autonomous Region are also described herein. Phylogenetic analyses based on the 18S rDNA and the D2–D3 region of the 28S rDNA support that the three new species are valid. The classifications of the families Tylencholaimellidae and Mydonomidae Thorne, 1964 are revised mainly based on the analysis of the morphology of odontostyle and odontophore. After these revisions, Paratylencholaiminae subfam. nov. including Paratylencholaimus gen. nov. and Goferus is proposed. Athernema and Agmodorus of Tylencholaimellidae are transferred into Mydonomidae, and the subfamily Athernematinae of Tylencholaimellidae is dismissed. The main characteristics of the family Mydonomidae and Tylencholaimellidae are revised. Keys to the genera of Mydomonidae and Tylencholaimellidae are included.
Wu et al. (2019) Three new species, one new genus and subfamily of Dorylaimida (de Man, 1876) Pearse, 1942, and revisions on the families Tylencholaimellidae Jairajpuri, 1964 and Mydonomidae Thorne, 1964 (Nematoda: Dorylaimida). PeerJ 7:e7541 https://doi.org/10.7717/peerj.7541
Cell-free supernatants from cultures of lactic acid bacteria isolated from fermented grape as biocontrol against Salmonella Typhi and Salmonella Typhimurium virulence via autoinducer-2 and biofilm interference
Background Salmonella Typhi and Salmonella Typhimurium are the causative pathogens of salmonellosis, and they are mostly found in animal source foods (ASF). The inappropriate use of antibiotics enhances the possibility for the emergence of antibiotic resistance in pathogens and antibiotic residue in ASF. One promising alternative to antibiotics in animal farming is the use of lactic acid bacteria (LAB). Methods The present study was carried out the cells and/or the cell-free culture supernatants (CFCS) from beneficial LAB against S. Typhi and S. Typhimurium. The antibacterial mechanisms of LAB-CFCS as biocontrol agents against both Salmonella serovars were investigated through the analysis of anti-salmonella growth activity, biofilm inhibition and quorum quenching activity. Results Among 146 LAB strains isolated from 110 fermented food samples, the 2 strong inhibitory effect strains (WM33 and WM36) from fermented grapes against both Salmonella serovars were selected. Out of the selected strains, WM36 was the most effective inhibitor, which indicated S. Typhi by showing 95.68% biofilm inhibition at 20% biofilm inhibition concentration (BIC) and reduced 99.84% of AI-2 signaling interference. The WM33 was the best to control S. Typhimurium by producing 66.46% biofilm inhibition at only 15% BIC and 99.99% AI-2 signaling a reduction. The 16S rDNA was amplified by a polymerase chain reaction (PCR). The selected isolates were identified as Weissella viridescens WM33 and Weissella confusa WM36 based on nucleotide homology and phylogenetic analysis. Conclusion The metabolic extracts from Weissella spp. inhibit Salmonella serovars with the potential to be used as biocontrol agents to improve microbiological safety in the production of ASF.
Pelyuntha et al. (2019) Cell-free supernatants from cultures of lactic acid bacteria isolated from fermented grape as biocontrol against Salmonella Typhi and Salmonella Typhimurium virulence via autoinducer-2 and biofilm interference. PeerJ 7:e7555 https://doi.org/10.7717/peerj.7555
Association between serum uric acid and nonalcoholic fatty liver disease in community patients with type 2 diabetes mellitus
Background To investigate whether SUA is associated with NAFLD in men and women with T2DM. Methods This cross-sectional study enrolled patients with T2DM at Shanxi High-Tech Development Zone Central Hospital (June 2011 to September 2017). Patients were stratified according to gender and presence/absence of NAFLD. Parameters associated with NAFLD were identified using multivariate stepwise linear regression and univariate/multivariate logistic regression. Results Among 597 patients (325 males) enrolled, 352 had NAFLD. SUA was higher in the NAFLD group than in the non-NAFLD group for both men and women (P < 0.001). Multiple linear regression showed that body mass index (positively), triglycerides (positively) and estimated glomerular filtration rate (negatively) were independently related to SUA (P < 0.001). Univariate logistic regression revealed increased odds of NAFLD for SUA tertiles 2 (P = 0.022) and 3 (P = 0.001) in women and tertile 3 (P = 0.039) in men. After adjustment for multiple clinical parameters, SUA tertiles were significantly associated with NAFLD for tertile 3 in women (P = 0.014), although there were trends toward associations for tertile 2 in women (P = 0.074) and tertiles 2 and 3 in men (P = 0.085 and 0.054, respectively). Conclusion SUA is not independently associated with NAFLD in men or women with T2DM after rigorous adjustment for other metabolic parameters.
Xu et al. (2019) Association between serum uric acid and nonalcoholic fatty liver disease in community patients with type 2 diabetes mellitus. PeerJ 7:e7563 https://doi.org/10.7717/peerj.7563
Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data
Background Mycobacterium tuberculosis rapid diagnostic tests (RDTs) are widely employed in routine laboratories and national surveys for detection of rifampicin-resistant (RR)-TB. However, as next-generation sequencing technologies have become more commonplace in research and surveillance programs, RDTs are being increasingly complemented by whole genome sequencing (WGS). While comparison between RDTs is difficult, all RDT results can be derived from WGS data. This can facilitate continuous analysis of RR-TB burden regardless of the data generation technology employed. By converting WGS to RDT results, we enable comparison of data with different formats and sources particularly for low- and middle-income high TB-burden countries that employ different diagnostic algorithms for drug resistance surveys. This allows national TB control programs (NTPs) and epidemiologists to utilize all available data in the setting for improved RR-TB surveillance. Methods We developed the Python-based MycTB Genome to Test (MTBGT) tool that transforms WGS-derived data into laboratory-validated results of the primary RDTs—Xpert MTB/RIF, XpertMTB/RIF Ultra, GenoType MDRTBplus v2.0, and GenoscholarNTM+MDRTB II. The tool was validated through RDT results of RR-TB strains with diverse resistance patterns and geographic origins and applied on routine-derived WGS data. Results The MTBGT tool correctly transformed the single nucleotide polymorphism (SNP) data into the RDT results and generated tabulated frequencies of the RDT probes as well as rifampicin-susceptible cases. The tool supplemented the RDT probe reactions output with the RR-conferring mutation based on identified SNPs. The MTBGT tool facilitated continuous analysis of RR-TB and Xpert probe reactions from different platforms and collection periods in Rwanda. Conclusion Overall, the MTBGT tool allows low- and middle-income countries to make sense of the increasingly generated WGS in light of the readily available RDT results, and assess whether currently implemented RDTs adequately detect RR-TB in their setting. With its feature to transform WGS to RDT results and facilitate continuous RR-TB data analysis, the MTBGT tool may bridge the gap between and among data from periodic surveys, continuous surveillance, research, and routine tests, and may be integrated within the national information system for use by the NTP and epidemiologists to improve setting-specific RR-TB control. The MTBGT source code and accompanying documentation are available at https://github.com/KamelaNg/MTBGT.
Ng et al. (2019) Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data. PeerJ 7:e7564 https://doi.org/10.7717/peerj.7564