DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data
For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and, as such, drives proteomics. MS/MS spectra need to be assigned a peptide sequence for which two strategies exist. Either database search or de novo sequencing can be employed to establish peptide spectrum matches. For database search, mzIdentML is the current community standard for data representation. There is no community standard for representing de novo sequencing results, but we previously proposed the de novo markup language (DNML). At the moment, each de novo sequencing solution uses different data representation, complicating downstream data integration, which is crucial since ensemble predictions may be more useful than predictions of a single tool. We here propose the de novo MS Ontology (DNMSO), which can, for example, provide many-to-many mappings between spectra and peptide predictions. Additionally, an application programming interface (API) that supports any file operation necessary for de novo sequencing from spectra input to reading, writing, creating, of the DNMSO format, as well as conversion from many other file formats, has been implemented. This API removes all overhead from the production of de novo sequencing tools and allows developers to concentrate on algorithm development completely. We make the API and formal descriptions of the format freely available at https://github.com/savastakan/dnmso.
Takan et al. (2020) DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data. PeerJ 8:e10216 https://doi.org/10.7717/peerj.10216
High microphone signal-to-noise ratio enhances acoustic sampling of wildlife
Background Automated sound recorders are a popular sampling tool in ecology. However, the microphones themselves received little attention so far, and specifications that determine the recordings’ sound quality are seldom mentioned. Here, we demonstrate the importance of microphone signal-to-noise ratio for sampling sonant animals. Methods We tested 12 different microphone models in the field and measured their signal-to-noise ratios and detection ranges. We also measured the vocalisation activity of birds and bats that they recorded, the bird species richness, the bat call types richness, as well as the performance of automated detection of bird and bat calls. We tested the relationship of each one of these measures with signal-to-noise ratio in statistical models. Results Microphone signal-to-noise ratio positively affects the sound detection space areas, which increased by a factor of 1.7 for audible sound, and 10 for ultrasound, from the lowest to the highest signal-to-noise ratio microphone. Consequently, the sampled vocalisation activity increased by a factor of 1.6 for birds, and 9.7 for bats. Correspondingly, the species pool of birds and bats could not be completely detected by the microphones with lower signal-to-noise ratio. The performance of automated detection of bird and bat calls, as measured by its precision and recall, increased significantly with microphone signal-to-noise ratio. Discussion Microphone signal-to-noise ratio is a crucial characteristic of a sound recording system, positively affecting the acoustic sampling performance of birds and bats. It should be maximised by choosing appropriate microphones, and be quantified independently, especially in the ultrasound range.
Darras et al. (2020) High microphone signal-to-noise ratio enhances acoustic sampling of wildlife. PeerJ 8:e9955 https://doi.org/10.7717/peerj.9955
Insect pollination is important in a smallholder bean farming system
Background Many crops are dependent on pollination by insects. Habitat management in agricultural landscapes can support pollinator services and even augment crop production. Common bean (Phaseolus vulgaris L.) is an important legume for the livelihoods of smallholder farmers in many low-income countries, particularly so in East Africa. While this crop is autogamous, it is frequently visited by pollinating insects that could improve yields. However, the value of pollination services to common beans (Kariasii) yield is not known. Methods We carried out pollinator-exclusion experiments to determine the contribution of insect pollinators to bean yields. We also carried out a fluorescent-dye experiment to evaluate the role of field margins as refuge for flower-visitors. Results Significantly higher yields, based on pods per plant and seeds per pod, were recorded from open-pollinated and hand-pollinated flowers compared to plants from which pollinators had been excluded indicating that flower visitors contribute significantly to bean yields. Similarly, open and hand-pollinated plants recorded the highest mean seed weight. Extrapolation of yield data to field scale indicated a potential increase per hectare from 681 kg in self-pollinated beans to 1,478 kg in open-pollinated beans indicating that flower visitors contributed significantly to crop yield of beans. Our marking study indicated that flower-visiting insects including bees, flies and lepidopterans moved from the field margin flowers into the bean crop. Overall, these results show that insect pollinators are important for optimising bean yields and an important food security consideration on smallholder farms. Field margin vegetation also provides habitat for flower-visiting insects that pollinate beans. Hence, non-crop habitats merit further research focusing on establishing which field margin species are most important and their capacity to support other ecosystem services such as natural pest regulation or even pests.
Elisante et al. (2020) Insect pollination is important in a smallholder bean farming system. PeerJ 8:e10102 https://doi.org/10.7717/peerj.10102
Isolation and evolutionary analyses of porcine epidemic diarrhea virus in Asia
Porcine epidemic diarrhea virus (PEDV) is a leading cause of diarrhea in pigs worldwide. Virus isolation and genetic evolutionary analysis allow investigations into the prevalence of epidemic strains and provide data for the clinical diagnosis and vaccine development. In this study, we investigated the genetic characteristics of PEDV circulation in Asia through virus isolation and comparative genomics analysis. APEDV strain designated HB2018 was isolated from a pig in a farm experiencing a diarrhea outbreak. The complete genome sequence of HB2018 was 28,138 bp in length. Phylogenetic analysis of HB2018 and 207 PEDVs in Asia showed that most PEDV strains circulating in Asia after 2010 belong to genotype GII, particularly GII-a. The PEDV vaccine strain CV777 belonged to GI, and thus, unmatched genotypes between CV777 and GII-a variants might partially explain incomplete protection by the CV777-derived vaccine against PEDV variants in China. In addition, we found the S protein of variant strains contained numerous mutations compared to the S protein of CV777, and these mutations occurred in the N-terminal domain of the S protein. These mutations may influence the antigenicity, pathogenicity, and neutralization properties of the variant strains.
Liang et al. (2020) Isolation and evolutionary analyses of porcine epidemic diarrhea virus in Asia. PeerJ 8:e10114 https://doi.org/10.7717/peerj.10114
Visual duration bisection in profoundly deaf individuals
Background Previous research has been designed to study the effect of hearing loss on supra-second duration estimation in the visual channel and position effect of visual abilities among deaf populations. The current study aimed to investigate the sub-second duration perception of different visual fields in profoundly deaf individuals. Methods A total of 16 profoundly deaf undergraduates and 16 hearing undergraduates completed a visual duration bisection task in which participants made judgments about whether a series of probe durations that were linearly spaced from 200 ms to 800 ms at 100 ms intervals were more similar to a standard short duration (200 ms) or a standard long duration (800 ms). The probe stimuli were presented in the center, left, or right of the screen. A repeated measure analysis of variance (ANOVA) with a between-participants factor of group and a within-participants factor of position, and a one-sample t-test were conducted. Results The Weber ratio (WR) values of deaf participants were significantly higher than those of hearing participants, regardless of the presented positions of the visual stimulus. The bisection point (BP) value of deaf participants was significantly lower than 500 ms (average mean of 200/800 ms) and the BP value of hearing participants did not significantly differ from 500 ms, although the overall difference of BP values between the deaf group and hearing group did not reach significance. For deaf participants, the BP value in the center condition was significantly lower than 500 ms; however, the difference between the BP value in the left condition and 500 ms did not reach significance, indicating that their duration discrimination accuracy in the left visual field was better than that in the center visual field. Conclusions Hearing loss impaired visual sub-second duration perception, and deaf individuals showed a left visual field advantage of duration discrimination accuracy during the visual duration bisection task.
Zhang et al. (2020) Visual duration bisection in profoundly deaf individuals. PeerJ 8:e10133 https://doi.org/10.7717/peerj.10133
Polarity and epithelial-mesenchymal transition of retinal pigment epithelial cells in proliferative vitreoretinopathy
Under physiological conditions, retinal pigment epithelium (RPE) is a cellular monolayer composed of mitotically quiescent cells. Tight junctions and adherens junctions maintain the polarity of RPE cells, and are required for cellular functions. In proliferative vitreoretinopathy (PVR), upon retinal tear, RPE cells lose cell-cell contact, undergo epithelial-mesenchymal transition (EMT), and ultimately transform into myofibroblasts, leading to the formation of fibrocellular membranes on both surfaces of the detached retina and on the posterior hyaloids, which causes tractional retinal detachment. In PVR, RPE cells are crucial contributors, and multiple signaling pathways, including the SMAD-dependent pathway, Rho pathway, MAPK pathways, Jagged/Notch pathway, and the Wnt/β-catenin pathway are activated. These pathways mediate the EMT of RPE cells, which play a key role in the pathogenesis of PVR. This review summarizes the current body of knowledge on the polarized phenotype of RPE, the role of cell-cell contact, and the molecular mechanisms underlying the RPE EMT in PVR, emphasizing key insights into potential approaches to prevent PVR.
Zou et al. (2020) Polarity and epithelial-mesenchymal transition of retinal pigment epithelial cells in proliferative vitreoretinopathy. PeerJ 8:e10136 https://doi.org/10.7717/peerj.10136
Mining the potential prognostic value of synaptosomal-associated protein 25 (SNAP25) in colon cancer based on stromal-immune score
Background Colon cancer is one of the deadliest tumors worldwide. Stromal cells and immune cells play important roles in cancer biology and microenvironment across different types of cancer. This study aimed to identify the prognostic value of stromal/immune cell-associated genes for colon cancer in The Cancer Genome Atlas (TCGA) database using bioinformatic technology. Methods The gene expression data and corresponding clinical information of colon cancer were downloaded from TCGA database. Stromal and immune scores were estimated based on the ESTIMATE algorithm. Sanger software was used to identify the differentially expressed genes (DEGs) and prognostic DEGs based on stromal and immune scores. External validation of prognostic biomarkers was conducted in Gene Expression Omnibus (GEO) database. Gene ontology (GO) analysis, pathway enrichment analysis, and gene set enrichment analysis (GSEA) were used for functional analysis. STRING and Cytoscape were used to assess the protein-protein interaction (PPI) network and screen hub genes. Quantitative real-time PCR (qRT-PCR) was used to validate the expression of hub genes in clinical tissues. Synaptosomal-associated protein 25 (SNAP25) was selected for analyzing its correlations with tumor-immune system in the TISIDB database. Results Worse overall survivals of colon cancer patients were found in high stromal score group (2963 vs. 1930 days, log-rank test P = 0.038) and high immune score group (2894 vs. 2230 days, log-rank test P = 0.076). 563 up-regulated and 9 down-regulated genes were identified as stromal-immune score-related DEGs. 70 up-regulated DEGs associated with poor outcomes were identified by COX proportional hazard regression model, and 15 hub genes were selected later. Then, we verified aquaporin 4 (AQP4) and SNAP25 as prognostic biomarkers in GEO database. qRT-PCR results revealed that AQP4 and SNAP25 were significantly elevated in colon cancer tissues compared with adjacent normal tissues (P = 0.003, 0.001). GSEA and TISIDB suggested that SNAP25 involved in cancer-related signaling pathway, immunity and metabolism progresses. Conclusion SNAP25 is a microenvironment-related and immune-related gene that can predict poor outcomes in colon cancer.
Zou et al. (2020) Mining the potential prognostic value of synaptosomal-associated protein 25 (SNAP25) in colon cancer based on stromal-immune score. PeerJ 8:e10142 https://doi.org/10.7717/peerj.10142
Mosasaurs were large, globally distributed aquatic lizards that lived during the Late Cretaceous. Despite numerous specimens of varying maturity, a detailed growth series has not been proposed for any mosasaur taxon. Two taxa—Tylosaurus proriger and T. kansasensis/nepaeolicus—have robust fossil records with specimens spanning a wide range of sizes and are thus ideal for studying mosasaur ontogeny. Tylosaurus is a genus of particularly large mosasaurs with long, edentulous anterior extensions of the premaxilla and dentary that lived in Europe and North America during the Late Cretaceous. An analysis of growth in Tylosaurus provides an opportunity to test hypotheses of the synonymy of T. kansasensis with T. nepaeolicus, sexual dimorphism, anagenesis, and heterochrony. Fifty-nine hypothetical growth characters were identified, including size-dependent, size-independent, and phylogenetic characters, and quantitative cladistic analysis was used to recover growth series for the two taxa. The results supported the synonymy of T. kansasensis with T. nepaeolicus and that T. kansasensis represent juveniles of T. nepaeolicus. A Spearman rank-order correlation test resulted in a significant correlation between two measures of size (total skull length and quadrate height) and maturity. Eleven growth changes were shared across both species, neither of the ontogram topologies showed evidence of skeletal sexual dimorphism, and a previous hypothesis of paedomorphy in T. proriger was not rejected. Finally, a novel hypothesis of anagenesis in Western Interior Seaway Tylosaurus species, driven by peramorphy, is proposed here.
Zietlow (2020) Craniofacial ontogeny in Tylosaurinae. PeerJ 8:e10145 https://doi.org/10.7717/peerj.10145
miR-29a-3p directly targets Smad nuclear interacting protein 1 and inhibits the migration and proliferation of cervical cancer HeLa cells
Smad nuclear interacting protein 1 (SNIP1) is a nuclear protein and involved in essential biological processes. MicroRNAs are effective regulators of tumorigenesis and cancer progression via targeting multiple genes. In present study, we aimed to investigate the function of SNIP1 and identify novel miRNA-SNIP1 axis in the development of cervical cancer. The results showed for the first time that silencing of the SNIP1 gene inhibited the migration and proliferation in HeLa cells significantly. Bioinformatics analysis and dual luciferase reporter assay demonstrated that miR-29a-3p could target 3′ UTR of SNIP1 directly. The mRNA and protein expression levels of SNIP1 were negative regulated by miR-29a-3p according to the RT-qPCR and Western blot analysis, respectively. Furthermore, functional studies showed that over-expression of miR-29a-3p restrained HeLa cells migration and proliferation, and the mRNA expression of SNIP1 downstream genes (HSP27, c-Myc, and cyclin D1) were down-regulated by miR-29a-3p. Together, we concluded that miR-29a-3p suppressed the migration and proliferation in HeLa cells by directly targeting SNIP1. The newly identified miR-29a-3p/SNIP1 axis could provide new insight into the development of cervical cancer.
Chen et al. (2020) miR-29a-3p directly targets Smad nuclear interacting protein 1 and inhibits the migration and proliferation of cervical cancer HeLa cells. PeerJ 8:e10148 https://doi.org/10.7717/peerj.10148
Spatiotemporal accumulation of fatal pharyngeal entrapment of flatfish in harbour porpoises (Phocoena phocoena) in the German North Sea
The evolution of a permanent separation of the upper respiratory and digestive tract is one of the adaptions cetaceans evolved for their aquatic life. Generally, it prevents odontocetes from choking on either saltwater or foreign bodies during ingestion under water. Nevertheless, several sporadic single case reports from different parts of the world show that this separation can be reversed especially by overly large items of prey. This incident can have a fatal outcome for the odontocetes. The German federal state of Schleswig-Holstein has a year-round, permanent and systematic stranding network that retrieves stranded marine mammals from its shorelines and constantly enables post-mortem examinations. In 2016, with nine affected animals, a high incidence of fatal pharyngeal entrapment of flatfish in harbour porpoises (Phocoena phocoena) occurred during spring and early summer on the German North Sea island of Sylt. All flatfish were identified as common sole (Solea solea). A retrospective post-mortem data analysis over a 30-year period from the North and Baltic Sea revealed similar yearly and seasonally case accumulations on the same island in the 1990s as well as several single case events over the whole timespan. All cases except one were caused by flatfish. When flatfish speciation was performed, only common sole was identified. From 1990 to 2019, of all examined harbour porpoises, 0.3% (2/713) from the Baltic Sea and 5.5% (45/820) from the North Sea died due to fish entrapped in the pharynx. On the North Sea coast, the occurrence of fatal obstruction shows high yearly variations from 0 to 33.3%. Years that stand out are especially 1990 to 1992, 1995, as well as 2016. The majority of all cases generally occurred between April and July, indicating also a seasonality of cases. This study evaluates the occurrence of fatal pharyngeal entrapment of fish in two geographically separated harbour porpoise populations. Additionally, common sole is clearly identified as a potentially risky item of prey for these small odontocetes.
Gross et al. (2020) Spatiotemporal accumulation of fatal pharyngeal entrapment of flatfish in harbour porpoises (Phocoena phocoena) in the German North Sea. PeerJ 8:e10160 https://doi.org/10.7717/peerj.10160