title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1425 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Duplicated flavonoid 3’-hydroxylase and flavonoid 3’, 5’-hydroxylase genes in barley genome link: https://peerj.com/articles/6266 last-modified: 2019-01-15 description: BackgroundAnthocyanin compounds playing multiple biological functions can be synthesized in different parts of barley (Hordeum vulgare L.) plant. The diversity of anthocyanin molecules is related with branching the pathway to alternative ways in which dihydroflavonols may be modified either with the help of flavonoid 3′-hydroxylase (F3′H) or flavonoid 3′,5′-hydroxylase (F3′5′H)—the cytochrome P450-dependent monooxygenases. The F3′H and F3′5′H gene families are among the least studied anthocyanin biosynthesis structural genes in barley. The aim of this study was to identify and characterise duplicated copies of the F3′H and F3′5′H genes in the barley genome.ResultsFour copies of the F3′5′H gene (on chromosomes 4HL, 6HL, 6HS and 7HS) and two copies of the F3′H gene (on chromosomes 1HL and 6HS) were identified in barley genome. These copies have either one or two introns. Amino acid sequences analysis demonstrated the presence of the flavonoid hydroxylase-featured conserved motifs in all copies of the F3′H and F3′5′H genes with the exception of F3′5′H-3 carrying a loss-of-function mutation in a conservative cytochrome P450 domain. It was shown that the divergence between F3′H and F3′5′H genes occurred 129 million years ago (MYA) before the emergence of monocot and dicot plant species. The F3′H copy approximately occurred 80 MYA; the appearance of F3′5′H copies occurred 8, 36 and 91 MYA. qRT-PCR analysis revealed the tissue-specific activity for some copies of the studied genes. The F3′H-1 gene was transcribed in aleurone layer, lemma and pericarp (with an increased level in the coloured pericarp), whereas the F3′H-2 gene was expressed in stems only. The F3′5′H-1 gene was expressed only in the aleurone layer, and in a coloured aleurone its expression was 30-fold higher. The transcriptional activity of F3′5′H-2 was detected in different tissues with significantly higher level in uncoloured genotype in contrast to coloured ones. The F3′5′H-3 gene expressed neither in stems nor in aleurone layer, lemma and pericarp. The F3′5′H-4 gene copy was weakly expressed in all tissues analysed.ConclusionF3′H and F3′5′H-coding genes involved in anthocyanin synthesis in H. vulgare were identified and characterised, from which the copies designated F3′H-1, F3′H-2, F3′5′H-1 and F3′5′H-2 demonstrated tissue-specific expression patterns. Information on these modulators of the anthocyanin biosynthesis pathway can be used in future for manipulation with synthesis of diverse anthocyanin compounds in different parts of barley plant. Finding both the copies with tissue-specific expression and a copy undergoing pseudogenization demonstrated rapid evolutionary events tightly related with functional specialization of the duplicated members of the cytochrome P450-dependent monooxygenases gene families. creator: Alexander V. Vikhorev creator: Ksenia V. Strygina creator: Elena K. Khlestkina uri: https://doi.org/10.7717/peerj.6266 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Vikhorev et al. title: Opioid distribution trends (2006–2017) in the US Territories link: https://peerj.com/articles/6272 last-modified: 2019-01-15 description: BackgroundThe US mainland is experiencing an epidemic of opioid overdoses. Unfortunately, the US Territories (Guam, Puerto Rico, and the Virgin Islands) have often been overlooked in opioid pharmacoepidemiology research. This study examined common prescription opioids over the last decade.MethodsThe United States Drug Enforcement Administration’s Automation of Reports and Consolidated Orders System (ARCOS) was used to report on ten medical opioids: buprenorphine, codeine, fentanyl, hydrocodone, hydromorphone, meperidine, methadone, morphine, oxycodone, and oxymorphone, by weight from 2006 to 2017. Florida and Hawaii were selected as comparison areas.ResultsPuerto Rico had the greatest Territorial oral morphine mg equivalent (MME) per capita (421.5) which was significantly higher (p < .005) than the Virgin Islands (139.2) and Guam (118.9) but significantly lower than that of Hawaii (794.6) or Florida (1,509.8). Methadone was the largest opioid by MMEs in 2017 in most municipalities, accounting for 41.1% of the total in the Virgin Islands, 37.9% in Florida, 36.6% in Hawaii but 80.8% in Puerto Rico. Puerto Rico and Florida showed pronounced differences in the distribution patterns by pharmacies, hospitals, and narcotic treatment programs for opioids.ConclusionsContinued monitoring of the US Territories is needed to provide a balance between appropriate access to these important agents for cancer related and acute pain while also minimizing diversion and avoiding the opioid epidemic which has adversely impacted the US mainland. creator: Fedor F. Cabrera creator: Erik R. Gamarra creator: Tiffany E. Garcia creator: Ashanti D. Littlejohn creator: Poul A. Chinga creator: Luis D. Pinentel-Morillo creator: Jorge R. Tirado creator: Daniel Y. Chung creator: Leana J. Pande creator: Kenneth L. McCall creator: Stephanie D. Nichols creator: Brian J. Piper uri: https://doi.org/10.7717/peerj.6272 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Cabrera et al. title: Estimating the incidence and diagnosed proportion of HIV infections in Japan: a statistical modeling study link: https://peerj.com/articles/6275 last-modified: 2019-01-15 description: BackgroundEpidemiological surveillance of HIV infection in Japan involves two technical problems for directly applying a classical backcalculation method, i.e., (i) all AIDS cases are not counted over time and (ii) people diagnosed with HIV have received antiretroviral therapy, extending the incubation period. The present study aimed to address these issues and estimate the HIV incidence and the proportion of diagnosed HIV infections, using a simple statistical model.MethodsFrom among Japanese nationals, yearly incidence data of HIV diagnoses and patients with AIDS who had not previously been diagnosed as HIV positive, from 1985 to 2017, were analyzed. Using the McKendrick partial differential equation, general convolution-like equations were derived, allowing estimation of the HIV incidence and the time-dependent rate of diagnosis. A likelihood-based approach was used to obtain parameter estimates.ResultsAssuming that the median incubation period was 10.0 years, the cumulative number of HIV infections was estimated to be 29,613 (95% confidence interval (CI): 29,059, 30,167) by the end of 2017, and the proportion of diagnosed HIV infections was estimated at 80.3% (95% CI [78.7%–82.0%]). Allowing the median incubation period to range from 7.5 to 12.3 years, the estimate of the proportion diagnosed can vary from 77% to 84%.DiscussionThe proportion of diagnosed HIV infections appears to have not yet reached 90% among Japanese nationals. Compared with the peak incidence from 2005–2008, new HIV infections have clearly been in a declining trend; however, there are still more than 1,000 new HIV infections per year in Japan. To increase the diagnosed proportion of HIV infections, it is critical to identify people who have difficulty accessing consultation, testing, and care, and to explore heterogeneous patterns of infection. creator: Hiroshi Nishiura uri: https://doi.org/10.7717/peerj.6275 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Nishiura title: Identification and characterization of capsule depolymerase Dpo48 from Acinetobacter baumannii phage IME200 link: https://peerj.com/articles/6173 last-modified: 2019-01-14 description: BackgroundThe emergence of multidrug- or extensively drug-resistant Acinetobacter baumannii has made it difficult to treat and control infections caused by this bacterium. It is urgently necessary to search for alternatives to conventional antibiotics for control of severe A. baumannii infections. In recent years, bacteriophages and their derivatives, such as depolymerases, showed great potential as antibacterial or antivirulence agents against bacterial infections. Nonetheless, unlike broad-spectrum bactericidal antibiotics, phage-encoded depolymerase targets only a limited number of bacterial strains. Therefore, identification of novel depolymerases and evaluation of their ability to control A. baumannii infections is important.MethodsA bacteriophage was isolated from hospital sewage using an extensively drug-resistant A. baumannii strain as the host bacterium, and the phage’s plaque morphology and genomic composition were studied. A polysaccharide depolymerase (Dpo48) was expressed and identified, and the effects of pH and temperature on its activity were determined. Besides, a serum killing assay was conducted, and amino acid sequences homologous to those of putative polysaccharide depolymerases were compared.ResultsPhage IME200 yielded clear plaques surrounded by enlarged halos, with polysaccharide depolymerase activity against the host bacterium. A tail fiber protein with a Pectate_lyase_3 domain was identified as Dpo48 and characterized . Dpo48 was found to degrade the capsule polysaccharide of the bacterial surface, as revealed by Alcian blue staining. Dpo48 manifested stable activity over a broad range of pH (5.0–9.0) and temperatures (20–70 °C). Results from in vitro serum killing assays indicated that 50% serum was sufficient to cause a five log reduction of overnight enzyme-treated bacteria, with serum complement playing an important role in these killing assays. Moreover, Dpo48 had a spectrum of activity exactly the same as its parental phage IME200, which was active against 10 out of 41 A. baumannii strains. Amino acid sequence alignment showed that the putative tail fiber proteins had a relatively short, highly conserved domain in their N-terminal sequences, but their amino acid sequences containing pectate lyase domains, found in the C-terminal regions, were highly diverse.ConclusionsPhage-encoded capsule depolymerases may become promising antivirulence agents for preventing and controlling A. baumannii infections. creator: Yannan Liu creator: Zhiqiang Mi creator: Liyuan Mi creator: Yong Huang creator: Puyuan Li creator: Huiying Liu creator: Xin Yuan creator: Wenkai Niu creator: Ning Jiang creator: Changqing Bai creator: Zhancheng Gao uri: https://doi.org/10.7717/peerj.6173 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Liu et al. title: Application of built-in adjuvants for epitope-based vaccines link: https://peerj.com/articles/6185 last-modified: 2019-01-14 description: Several studies have shown that epitope vaccines exhibit substantial advantages over conventional vaccines. However, epitope vaccines are associated with limited immunity, which can be overcome by conjugating antigenic epitopes with built-in adjuvants (e.g., some carrier proteins or new biomaterials) with special properties, including immunologic specificity, good biosecurity and biocompatibility, and the ability to vastly improve the immune response of epitope vaccines. When designing epitope vaccines, the following types of built-in adjuvants are typically considered: (1) pattern recognition receptor ligands (i.e., toll-like receptors); (2) virus-like particle carrier platforms; (3) bacterial toxin proteins; and (4) novel potential delivery systems (e.g., self-assembled peptide nanoparticles, lipid core peptides, and polymeric or inorganic nanoparticles). This review primarily discusses the current and prospective applications of these built-in adjuvants (i.e., biological carriers) to provide some references for the future design of epitope-based vaccines. creator: Yao Lei creator: Furong Zhao creator: Junjun Shao creator: Yangfan Li creator: Shifang Li creator: Huiyun Chang creator: Yongguang Zhang uri: https://doi.org/10.7717/peerj.6185 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Lei et al. title: Worldwide co-occurrence analysis of 17 species of the genus Brachypodium using data mining link: https://peerj.com/articles/6193 last-modified: 2019-01-14 description: The co-occurrence of plant species is a fundamental aspect of plant ecology that contributes to understanding ecological processes, including the establishment of ecological communities and its applications in biological conservation. A priori algorithms can be used to measure the co-occurrence of species in a spatial distribution given by coordinates. We used 17 species of the genus Brachypodium, downloaded from the Global Biodiversity Information Facility data repository or obtained from bibliographical sources, to test an algorithm with the spatial points process technique used by Silva et al. (2016), generating association rules for co-occurrence analysis. Brachypodium spp. has emerged as an effective model for monocot species, growing in different environments, latitudes, and elevations; thereby, representing a wide range of biotic and abiotic conditions that may be associated with adaptive natural genetic variation. We created seven datasets of two, three, four, six, seven, 15, and 17 species in order to test the algorithm with four different distances (1, 5, 10, and 20 km). Several measurements (support, confidence, lift, Chi-square, and p-value) were used to evaluate the quality of the results generated by the algorithm. No negative association rules were created in the datasets, while 95 positive co-occurrences rules were found for datasets with six, seven, 15, and 17 species. Using 20 km in the dataset with 17 species, we found 16 positive co-occurrences involving five species, suggesting that these species are coexisting. These findings are corroborated by the results obtained in the dataset with 15 species, where two species with broad range distributions present in the previous dataset are eliminated, obtaining seven positive co-occurrences. We found that B. sylvaticum has co-occurrence relations with several species, such as B. pinnatum, B. rupestre, B. retusum, and B. phoenicoides, due to its wide distribution in Europe, Asia, and north of Africa. We demonstrate the utility of the algorithm implemented for the analysis of co-occurrence of 17 species of the genus Brachypodium, agreeing with distributions existing in nature. Data mining has been applied in the field of biological sciences, where a great amount of complex and noisy data of unseen proportion has been generated in recent years. Particularly, ecological data analysis represents an opportunity to explore and comprehend biological systems with data mining and bioinformatics tools. creator: Simon Orozco-Arias creator: Ana María Núñez-Rincón creator: Reinel Tabares-Soto creator: Diana López-Álvarez uri: https://doi.org/10.7717/peerj.6193 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Orozco-Arias et al. title: Combining legacy data with new drone and DGPS mapping to identify the provenance of Plio-Pleistocene fossils from Bolt’s Farm, Cradle of Humankind (South Africa) link: https://peerj.com/articles/6202 last-modified: 2019-01-14 description: Bolt’s Farm is a Plio-Pleistocene fossil site located within the southwestern corner of the UNESCO Hominid Fossil Sites of South Africa World Heritage Site. The site is a complex of active caves and more than 20 palaeokarst deposits or pits, many of which were exposed through the action of lime mining in the early 20th century. The pits represent heavily eroded cave systems, and as such associating the palaeocave sediments within and between the pits is difficult, especially as little geochronological data exists. These pits and the associated lime miner’s rubble were first explored by palaeoanthropologists in the late 1930s, but as yet no hominin material has been recovered. The first systematic mapping was undertaken by Frank Peabody as part of the University of California Africa Expedition (UCAE) in 1947–1948. A redrawn version of the map was not published until 1991 by Basil Cooke and this has subsequently been used and modified by recent researchers. Renewed work in the 2000s used Cooke’s map to try and relocate the original fossil deposits. However, Peabody’s map does not include all the pits and caves, and thus in some cases this was successful, while in others previously sampled pits were inadvertently given new names. This was compounded by the fact that new fossil bearing deposits were discovered in this new phase, causing confusion in associating the 1940s fossils with the deposits from which they originated; as well as associating them with the recently excavated material. To address this, we have used a Geographic Information System (GIS) to compare Peabody’s original map with subsequently published maps. This highlighted transcription errors between maps, most notably the location of Pit 23, an important palaeontological deposit given the recovery of well-preserved primate crania (Parapapio, Cercopithecoides) and partial skeletons of the extinct felid Dinofelis. We conducted the first drone and Differential Global Positioning System (DGPS) survey of Bolt’s Farm. Using legacy data, high-resolution aerial imagery, accurate DGPS survey and GIS, we relocate the original fossil deposits and propose a definitive and transparent naming strategy for Bolt’s Farm, based on the original UCAE Pit numbers. We provide datum points and a new comprehensive, georectified map to facilitate spatially accurate fossil collection for all future work. Additionally, we have collated recently published faunal data with historic fossil data to evaluate the biochronological potential of the various deposits. This suggests that the palaeocave deposits in different pits formed at different times with the occurrence of Equus in some pits implying ages of <2.3 Ma, whereas more primitive suids (Metridiochoerus) hint at a terminal Pliocene age for other deposits. This study highlights that Bolt’s Farm contains rare South African terminal Pliocene fossil deposits and creates a framework for future studies of the deposits and previously excavated material. creator: Tara R. Edwards creator: Brian J. Armstrong creator: Jessie Birkett-Rees creator: Alexander F. Blackwood creator: Andy I.R. Herries creator: Paul Penzo-Kajewski creator: Robyn Pickering creator: Justin W. Adams uri: https://doi.org/10.7717/peerj.6202 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2019 Edwards et al. title: Using lidar to assess the development of structural diversity in forests undergoing passive rewilding in temperate Northern Europe link: https://peerj.com/articles/6219 last-modified: 2019-01-14 description: Forested areas are increasing across Europe, driven by both reforestation programs and farmland abandonment. While tree planting remains the standard reforestation strategy, there is increased interest in spontaneous regeneration as a cost-effective method with equal or potentially greater benefits. Furthermore, expanding areas of already established forests are left for passive rewilding to promote biodiversity conservation. Effective and objective methods are needed for monitoring and analyzing the development of forest structure under these management scenarios, with airborne laser scanning (lidar: light detection and ranging) being a promising methodology. Here, we assess the structural characteristics and development of unmanaged forests and 28- to 78-year old spontaneously regenerated forests on former agricultural land, relative to managed forests of similar age in Denmark, using 25 lidar-derived metrics in 10- and 30-m grid cells. We analyzed the lidar-derived cell values in a principal component analysis (PCA) and interpreted the axes ecologically, in conjunction with pairwise tests of median and variance of PCA-values for each forest. Spontaneously regenerated forest in general had increased structural heterogeneity compared to planted and managed forests. Furthermore, structural heterogeneity kept increasing in spontaneously regenerated forest across the maximal 78-year timespan investigated. Natural disturbances showed strong impacts on vegetation structure, leading to both structural homogeneity and heterogeneity. The results illustrate the utility of passive rewilding for generating structurally heterogeneous forested nature areas, and the utility of lidar surveys for monitoring and interpreting structural development of such forests. creator: Henrik Thers creator: Peder Klith Bøcher creator: Jens-Christian Svenning uri: https://doi.org/10.7717/peerj.6219 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Thers et al. title: Global genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments link: https://peerj.com/articles/6233 last-modified: 2019-01-14 description: BackgroundThe Streptococcus genus is relevant to both public health and food safety because of its ability to cause pathogenic infections. It is well-represented (>100 genomes) in publicly available databases. Streptococci are ubiquitous, with multiple sources of isolation, from human pathogens to dairy products. The Streptococcus genus has traditionally been classified by morphology, serum types, the 16S ribosomal RNA (rRNA) gene, and multi-locus sequence types subject to in-depth comparative genomic analysis.MethodsCore and pan-genomes described the genomic diversity of 108 strains belonging to 16 Streptococcus species. The core genome nucleotide diversity was calculated and compared to phylogenomic distances within the genus Streptococcus. The core genome was also used as a resource to recruit metagenomic fragment reads from streptococci dominated environments. A conventional 16S rRNA gene phylogeny reconstruction was used as a reference to compare the resulting dendrograms of average nucleotide identity (ANI) and genome similarity score (GSS) dendrograms.ResultsThe core genome, in this work, consists of 404 proteins that are shared by all 108 Streptococcus. The average identity of the pairwise compared core proteins decreases proportionally to GSS lower scores, across species. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). The GSS is a distance metric that can reflect evolutionary history comparing orthologous proteins. Additionally, GSS resulted in the most useful metric for genus and species comparisons, where ANI metrics failed due to false positives when comparing different species.DiscussionUnderstanding of genomic variability and species relatedness is the goal of tools like GSS, which makes use of the maximum pairwise shared orthologous sequences for its calculation. It allows for long evolutionary distances (above species) to be included because of the use of amino acid alignment scores, rather than nucleotides, and normalizing by positive matches. Newly sequenced species and strains could be easily placed into GSS dendrograms to infer overall genomic relatedness. The GSS is not restricted to ubiquitous conservancy of gene features; thus, it reflects the mosaic-structure and dynamism of gene acquisition and loss in bacterial genomes. creator: Hugo R. Barajas creator: Miguel F. Romero creator: Shamayim Martínez-Sánchez creator: Luis D. Alcaraz uri: https://doi.org/10.7717/peerj.6233 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Barajas et al. title: Method for the quantitative evaluation of ecosystem services in coastal regions link: https://peerj.com/articles/6234 last-modified: 2019-01-14 description: Wetlands, tidal flats, seaweed beds, and coral reefs are valuable not only as habitats for many species, but also as places where people interact with the sea. Unfortunately, these areas have declined in recent years, so environmental improvement projects to conserve and restore them are being carried out across the world. In this study, we propose a method for quantifying ecosystem services, that is, useful for the proper maintenance and management of artificial tidal flats, a type of environmental improvement project. With this method, a conceptual model of the relationship between each service and related environmental factors in natural and social systems was created, and the relationships between services and environmental factors were clarified. The state of the environmental factors affecting each service was quantified, and the state of those factors was reflected in the evaluation value of the service. As a result, the method can identify which environmental factors need to be improved and if the goal is to increase the value of the targeted tidal flat. The method demonstrates an effective approach in environmental conservation for the restoration and preservation of coastal areas. creator: Tomonari Okada creator: Yugo Mito creator: Erina Iseri creator: Toshiyuki Takahashi creator: Takanori Sugano creator: Yoshihiro B. Akiyama creator: Kenta Watanabe creator: Toko Tanaya creator: Hiroaki Sugino creator: Kanae Tokunaga creator: Takahiro Kubo creator: Tomohiro Kuwae uri: https://doi.org/10.7717/peerj.6234 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2019 Okada et al.