title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1087 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: OBAMA: OBAMA for Bayesian amino-acid model averaging link: https://peerj.com/articles/9460 last-modified: 2020-08-04 description: BackgroundBayesian analyses offer many benefits for phylogenetic, and have been popular for analysis of amino acid alignments. It is necessary to specify a substitution and site model for such analyses, and often an ad hoc, or likelihood based method is employed for choosing these models that are typically of no interest to the analysis overall.MethodsWe present a method called OBAMA that averages over substitution models and site models, thus letting the data inform model choices and taking model uncertainty into account. It uses trans-dimensional Markov Chain Monte Carlo (MCMC) proposals to switch between various empirical substitution models for amino acids such as Dayhoff, WAG, and JTT. Furthermore, it switches base frequencies from these substitution models or use base frequencies estimated based on the alignment. Finally, it switches between using gamma rate heterogeneity or not, and between using a proportion of invariable sites or not.ResultsWe show that the model performs well in a simulation study. By using appropriate priors, we demonstrate both proportion of invariable sites and the shape parameter for gamma rate heterogeneity can be estimated. The OBAMA method allows taking in account model uncertainty, thus reducing bias in phylogenetic estimates. The method is implemented in the OBAMA package in BEAST 2, which is open source licensed under LGPL and allows joint tree inference under a wide range of models. creator: Remco R. Bouckaert uri: https://doi.org/10.7717/peerj.9460 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Bouckaert title: Survival, growth and carbon content in a forest plantation established after a clear-cutting in Durango, Mexico link: https://peerj.com/articles/9506 last-modified: 2020-08-04 description: BackgroundForest plantations play an important role in carbon sequestration, helping to mitigate climate change. In this study, survival, biomass, growth rings and annual carbon content storage were evaluated in a mixed Pinus durangensis and P. cooperi plantation that was established after a clear-cutting. The plantation is eight years old and covers an area of 21.40 ha.MethodsSixteen sites of 100 m2 were distributed randomly. At each site, two trees distributed proportionally to the diametric categories were destructively sampled (one per tree species). Two cross-sections were cut from each tree: The first at the base of the stump and the second at 1.30 m. The width of tree rings of the first cross-section was measured using a stereoscopic microscope with precision in microns (µm). The year-by-year basal diameter of each tree was recorded and biomass and carbon content was estimated using allometric equations.ResultsThe estimated survival was 75.2%. The results of the ANOVA showed significant differences between the year-by-year width records of tree rings, the highest value corresponding to the fifth year. The average carbon sequestration per year is 0.30 kg for both studied tree species.ConclusionsP. durangensis and P. cooperi plantations adapt and develop well in Durango forests when they are established in areas that are subjected to clear-cutting. creator: Jesús Alejandro Soto-Cervantes creator: Artemio Carrillo-Parra creator: Rodrigo Rodríguez-Laguna creator: José Javier Corral-Rivas creator: Marín Pompa-García creator: Pedro Antonio Dominguez-Calleros uri: https://doi.org/10.7717/peerj.9506 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Soto-Cervantes et al. title: Identifying agricultural pesticides that may pose a risk for birds link: https://peerj.com/articles/9526 last-modified: 2020-08-04 description: In this study, we analyze changing patterns of pesticide use in agriculture in Great Britain over the 1990–2016 period, with respect to the risk they pose to birds. The weight of pesticides applied decreased by 51% between 1990 and 2016, but the area treated increased by 63% over the same period. Over this period, there has been considerable turnover in the pesticides used. The European Union (including Great Britain until 2020) has restricted or banned many pesticides for agricultural use, including organophosphates and carbamates. However, new generations of active substances have been introduced, such as the neonicotinoids, some of which have since been banned. In this analysis, we estimate the annual ‘toxic load’ of agricultural pesticide use in Great Britain for birds, measured as the total number of LD50 doses for corn buntings, Emberiza calandra. We have previously performed similar analyses for bees, for which the total toxic load increased six-fold during this period. In contrast, for birds the total toxic load fell by 80.5%, although still correspond to 8.3e+11 corn bunting LD50 doses in 2016. The decrease in toxicity is largely due to declining use of highly toxic organophosphates in recent years. We identify the pesticides in current use that may pose the highest risk to birds, which include a mix of insecticides, herbicides, fungicides, molluscicides, acaricides and plant growth regulators. The insecticide ethoprop was ranked highest in 2016, with a toxic load of 71 billion potential corn bunting kills. Some of the other chemicals presenting a high toxic load, such as the herbicide chlormequat, are not highly toxic to birds (in terms of LD50) but are used in very large quantities. However, it is important to stress that, in reality, only a tiny proportion of pesticides applied will be ingested by birds, and this will vary according to timing and method of application, persistence of the active substance and many other factors. We further note that impacts of pesticides on birds might often be indirect, for example via depleting their food supply, and that sublethal impacts may occur at much lower doses than the LD50, neither of which do we investigate here. Nonetheless, we suggest that this is a useful approach to highlight pesticides that might be worth closer study with regard to possible impacts. creator: Cannelle Tassin de Montaigu creator: Dave Goulson uri: https://doi.org/10.7717/peerj.9526 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Tassin de Montaigu and Goulson title: Regional distribution of Christensenellaceae and its associations with metabolic syndrome based on a population-level analysis link: https://peerj.com/articles/9591 last-modified: 2020-08-04 description: The link between the gut microbiota and metabolic syndrome (MetS) has attracted widespread attention. Christensenellaceae was recently described as an important player in human health, while its distribution and relationship with MetS in Chinese population is still unknown. This study sought to observe the association between Christensenellaceae and metabolic indexes in a large sample of residents in South China. A total of 4,781 people from the GGMP project were included, and the fecal microbiota composition of these individuals was characterized by 16S rRNA sequencing and analyzed the relation between Christensenellaceae and metabolism using QIIME (Quantitative Insight Into Microbial Ecology, Version 1.9.1). The results demonstrated that microbial richness and diversity were increased in the group with a high abundance of Christensenellaceae, who showed a greater complexity of the co-occurrence network with other bacteria than residents who lacked Christensenellaceae. The enriched bacterial taxa were predominantly represented by Oscillospira, Ruminococcaceae, RF39, Rikenellaceae and Akkermansia as the Christensenellaceae abundance increased, while the abundances of Veillonella, Fusobacterium and Klebsiella were significantly reduced. Furthermore, Christensenellaceae was negatively correlated with the pathological features of MetS, such as obesity, hypertriglyceridemia and body mass index (BMI). We found reduced levels of lipid biosynthesis and energy metabolism pathways in people with a high abundance of Christensenellaceae, which may explain the negative relationship between body weight and Christensenellaceae. In conclusion, we found a negative correlation between Christensenellaceae and MetS in a large Chinese population and reported the geographical distribution of Christensenellaceae in the GGMP study. The association data from this population-level research support the investigation of strains within Christensenellaceae as potentially beneficial gut microbes. creator: Xiang Li creator: Zewen Li creator: Yan He creator: Pan Li creator: Hongwei Zhou creator: Nianyi Zeng uri: https://doi.org/10.7717/peerj.9591 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Li et al. title: Proteins from Lignosus tigris with selective apoptotic cytotoxicity towards MCF7 cell line and suppresses MCF7-xenograft tumor growth link: https://peerj.com/articles/9650 last-modified: 2020-08-04 description: BackgroundLignosus tigris, a recently discovered species of the unique Lignosus family, has been traditionally used by the indigenous communities in Peninsular Malaysia to treat various ailments and as an alternative medicine for cancer treatment. The L. tigris cultivar sclerotia (Ligno TG-K) was found to contain numerous bioactive compounds with beneficial biomedicinal properties and the sclerotial extract exhibited potent antioxidant activity. However, the anticancer property of the Ligno TG-K including in vitro and in vivo antitumor effects as well as its anticancer active compounds and the mechanisms has yet to be investigated.MethodsThe cytotoxicity of the Ligno TG-K against human breast (MCF7), prostate (PC3) and lung (A549) adenocarcinoma cell lines was evaluated using MTT cytotoxicity assay. The cytotoxic mechanisms of the active high molecular weight proteins (HMWp) fraction were investigated through detection of caspases activity and apoptotic-related proteins expression by Western blotting. The in vivo antitumor activity of the isolated HMWp was examined using MCF7 mouse xenograft model. Shotgun LC-MS/MS analysis was performed to identify the proteins in the HMWp.Results and DiscussionCold water extract of the sclerotia inhibited proliferation of MCF7, A549 and PC3 cells with IC50 ranged from 28.9 to 95.0 µg/mL. Bioassay guided fractionation of the extract revealed that HMWp exhibited selective cytotoxicity against MCF7 cells via induction of cellular apoptosis by the activation of extrinsic and intrinsic signaling pathways. HMWp activated expression of caspase-8 and -9 enzymes, and pro-apoptotic Bax protein whilst inhibiting expression of tumor survivor protein, Bcl-2. HMWp induced tumor-cell apoptosis and suppressed growth of tumor in MCF-7 xenograft mice. Lectins, serine proteases, RNase Gf29 and a 230NA deoxyribonuclease are the major cytotoxic proteins that accounted for 55.93% of the HMWp.ConclusionThe findings from this study provided scientific evidences to support the traditional use of the L. tigris sclerotia for treatment of breast cancer. Several cytotoxic proteins with high abundance have been identified in the HMWp of the sclerotial extract and these proteins have potential to be developed into new anticancer agents or as adjunct cancer therapy. creator: Boon Hong Kong creator: Kean Hooi Teoh creator: Nget Hong Tan creator: Chon Seng Tan creator: Szu Ting Ng creator: Shin Yee Fung uri: https://doi.org/10.7717/peerj.9650 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Kong et al. title: Taxonomic affiliation influences the selection of medicinal plants among people from semi-arid and humid regions—a proposition for the evaluation of utilitarian equivalence in Northeast Brazil link: https://peerj.com/articles/9664 last-modified: 2020-08-04 description: BackgroundThis study sought to investigate the occurrence of taxonomic patterns between semi-arid and humid regions, verifying how the taxonomic affiliation can influence the selection of plants for medicinal purposes and act as a selection criterion.MethodsThe relationship between the taxonomic affiliation and the selection of medicinal plants with four different communities was analyzed; two of them associated with a seasonally dry tropical forest and the other two associated with a tropical rain forest. We used the Utilitarian Equivalence Model (transposing the concept of ecological equivalence, proposed by Odum, for ethnobotany) to test the hypothesis that species that have the same taxonomic affiliation tend to have the same therapeutic applications in different environments (utilitarian equivalence). In addition, we used the Utilitarian Redundancy Model to verify whether, within the same medical system, plants of the same taxonomic affiliation tend to be redundant (treating the same diseases).ResultsWe found that a pair of plants of the same genus were 9.25 times more likely to be equivalent than a different genus pair (OR = 9.25, CI [1.68–51.02], p < 0.05). When we analyzed the species used by the same population, the chances of a pair having similar therapeutic uses (utilitarian redundancy) increased when they were species of the same family (OR = 1.94, CI [1.06−3.53]; p < 0.05).ConclusionsThese findings confirm the hypothesis that there is an influence of taxonomic affiliation, in terms of genera and family, on the selection of medicinal plants in semi-arid and humid areas in Northeast Brazil. In addition, our Utilitarian Equivalence Model can be an important tool in the search for more common selection criteria, in order to identify the shared characteristics among the equivalent pairs and consequently the main types of perceptions or stimuli that led to the inclusion of such species in local pharmacopoeias. creator: Rafael Reinaldo creator: Ulysses Albuquerque creator: Patrícia Medeiros uri: https://doi.org/10.7717/peerj.9664 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Reinaldo et al. title: Spatial distribution and feeding substrate of butterflyfishes (family Chaetodontidae) on an Okinawan coral reef link: https://peerj.com/articles/9666 last-modified: 2020-08-04 description: Coral reefs support diverse communities, and relationships among organisms within these communities are quite complex. Among the relationships, clarifying the habitat association and foraging substrate selection relative to habitat characteristics is of central importance to ecology since these two aspects are the fundamentals for survival and growth of organisms. The aims of the present study were to investigate the spatial distribution and feeding substrate selection of 14 species of butterflyfishes on an Okinawan coral reef in Japan. Species-specific spatial distributions varied with habitat characteristics (e.g., encrusting corals, massive corals, branching Acropora and rock). For feeding substrates, seven species of obligate coral polyp feeders exhibited significant positive selectivity for tabular Acropora, corymbose Acropora, encrusting corals and massive corals but significant negative selectivity for dead corals, coral rubble and rock. Among six species of facultative coral polyp feeders, two species exhibited significant positive selectivity for encrusting corals and massive corals, and one species showed significant positive selectivity for dead corals as feeding substrates. In contrast, three species exhibited no significant positive selectivity for any feeding substrates. A similar result was observed for one non-coralline invertebrate feeder. Among the 14 species, 12 species showed a relatively close relationship between spatial distribution and feeding substrates but the remaining two species did not. The present study is the first study to elucidate species-specific spatial distributions and feeding substrate selection of butterflyfishes on an Okinawan coral reef. The results of the present study suggest that diverse substrates, including various types of living corals (especially encrusting corals, massive corals, tabular Acropora, corymbose Acropora and branching Acropora) and non-coralline substrates (rock) are the primary determinants of spatial distributions and feeding sites. Thus, diverse substrates are important for maintaining high species diversity of butterflyfishes and changes of the substrates would likely change the spatial patterns and foraging behavior, although species-specific responses may be found, depending on their species-specific dependence on vulnerable substrates. creator: Atsushi Nanami uri: https://doi.org/10.7717/peerj.9666 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Nanami title: Convolutional neural networks to automate the screening of malaria in low-resource countries link: https://peerj.com/articles/9674 last-modified: 2020-08-04 description: Malaria is an infectious disease caused by Plasmodium parasites, transmitted through mosquito bites. Symptoms include fever, headache, and vomiting, and in severe cases, seizures and coma. The World Health Organization reports that there were 228 million cases and 405,000 deaths in 2018, with Africa representing 93% of total cases and 94% of total deaths. Rapid diagnosis and subsequent treatment are the most effective means to mitigate the progression into serious symptoms. However, many fatal cases have been attributed to poor access to healthcare resources for malaria screenings. In these low-resource settings, the use of light microscopy on a thin blood smear with Giemsa stain is used to examine the severity of infection, requiring tedious and manual counting by a trained technician. To address the malaria endemic in Africa and its coexisting socioeconomic constraints, we propose an automated, mobile phone-based screening process that takes advantage of already existing resources. Through the use of convolutional neural networks (CNNs), we utilize a SSD multibox object detection architecture that rapidly processes thin blood smears acquired via light microscopy to isolate images of individual red blood cells with 90.4% average precision. Then we implement a FSRCNN model that upscales 32 × 32 low-resolution images to 128 × 128 high-resolution images with a PSNR of 30.2, compared to a baseline PSNR of 24.2 through traditional bicubic interpolation. Lastly, we utilize a modified VGG16 CNN that classifies red blood cells as either infected or uninfected with an accuracy of 96.5% in a balanced class dataset. These sequential models create a streamlined screening platform, giving the healthcare provider the number of malaria-infected red blood cells in a given sample. Our deep learning platform is efficient enough to operate exclusively on low-tier smartphone hardware, eliminating the need for high-speed internet connection. creator: Oliver S. Zhao creator: Nikhil Kolluri creator: Anagata Anand creator: Nicholas Chu creator: Ravali Bhavaraju creator: Aditya Ojha creator: Sandhya Tiku creator: Dat Nguyen creator: Ryan Chen creator: Adriane Morales creator: Deepti Valliappan creator: Juhi P. Patel creator: Kevin Nguyen uri: https://doi.org/10.7717/peerj.9674 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2020 Zhao et al. title: White-handed gibbons discriminate context-specific song compositions link: https://peerj.com/articles/9477 last-modified: 2020-08-03 description: White-handed gibbons produce loud and acoustically complex songs when interacting with their neighbours or when encountering predators. In both contexts, songs are assembled from a small number of units although their composition differs in context-specific ways. Here, we investigated whether wild gibbons could infer the ‘meaning’ when hearing exemplars recorded in both contexts (i.e. ‘duet songs’ vs. ‘predator songs’). We carried out a playback experiment by which we simulated the presence of a neighbouring group producing either its duet or a predator song in order to compare subjects’ vocal and locomotor responses. When hearing a recording of a duet song, subjects reliably responded with their own duet song, which sometimes elicited further duet songs in adjacent groups. When hearing a recording of a predator song, however, subjects typically remained silent, apart from one of six groups which replied with its own predator song. Moreover, in two of six trials, playbacks of predator songs elicited predator song replies in non-adjacent groups. Finally, all groups showed strong anti-predator behaviour to predator songs but never to duet songs. We concluded that white-handed gibbons discriminated between the two song types and were able to infer meaning from them. We discuss the implications of these findings in light of the current debate on the evolutionary origins of syntax. creator: Julie Andrieu creator: Samuel G. Penny creator: Hélène Bouchet creator: Suchinda Malaivijitnond creator: Ulrich H. Reichard creator: Klaus Zuberbühler uri: https://doi.org/10.7717/peerj.9477 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Andrieu et al. title: Anti-COVID-19 multi-epitope vaccine designs employing global viral genome sequences link: https://peerj.com/articles/9541 last-modified: 2020-08-03 description: BackgroundThe coronavirus SARS-CoV-2 is a member of the Coronaviridae family that has caused a global public health emergency. Currently, there is no approved treatment or vaccine available against it. The current study aimed to cover the diversity of SARS-CoV-2 strains reported from all over the world and to design a broad-spectrum multi-epitope vaccine using an immunoinformatics approach.MethodsFor this purpose, all available complete genomes were retrieved from GISAID and NGDC followed by genome multiple alignments to develop a global consensus sequence to compare with the reference genome. Fortunately, comparative genomics and phylogeny revealed a significantly high level of conservation between the viral strains. All the Open Reading Frames (ORFs) of the reference sequence NC_045512.2 were subjected to epitope mapping using CTLpred and HLApred, respectively. The predicted CTL epitopes were then screened for antigenicity, immunogenicity and strong binding affinity with HLA superfamily alleles. HTL predicted epitopes were screened for antigenicity, interferon induction potential, overlapping B cell epitopes and strong HLA DR binding potential. The shortlisted epitopes were arranged into two multi-epitope sequences, Cov-I-Vac and Cov-II-Vac, and molecular docking was performed with Toll-Like Receptor 8 (TLR8).ResultsThe designed multi-epitopes were found to be antigenic and non-allergenic. Both multi-epitopes were stable and predicted to be soluble in an Escherichia coli expression system. The molecular docking with TLR8 also demonstrated that they have a strong binding affinity and immunogenic potential. These in silico analyses suggest that the proposed multi-epitope vaccine can effectively evoke an immune response. creator: Tahreem Zaheer creator: Maaz Waseem creator: Walifa Waqar creator: Hamza Arshad Dar creator: Muhammad Shehroz creator: Kanwal Naz creator: Zaara Ishaq creator: Tahir Ahmad creator: Nimat Ullah creator: Syeda Marriam Bakhtiar creator: Syed Aun Muhammad creator: Amjad Ali uri: https://doi.org/10.7717/peerj.9541 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2020 Zaheer et al.