title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=991 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: In situ dissecting the evolution of gene duplication with different histone modification patterns based on high-throughput data analysis in Arabidopsis thaliana link: https://peerj.com/articles/10426 last-modified: 2021-01-05 description: BackgroundGenetic regulation is known to contribute to the divergent expression of duplicate genes; however, little is known about how epigenetic modifications regulate the expression of duplicate genes in plants.MethodsThe histone modification (HM) profile patterns of different modes of gene duplication, including the whole genome duplication, proximal duplication, tandem duplication and transposed duplication were characterized based on ChIP-chip or ChIP-seq datasets. In this study, 10 distinct HM marks including H2Bub, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H3K9me2, H3K27me1, H3K27me3, H3K36me3 and H3K14ac were analyzed. Moreover, the features of gene duplication with different HM patterns were characterized based on 88 RNA-seq datasets of Arabidopsis thaliana.ResultsThis study showed that duplicate genes in Arabidopsis have a more similar HM pattern than single-copy genes in both their promoters and protein-coding regions. The evolution of HM marks is found to be coupled with coding sequence divergence and expression divergence after gene duplication. We found that functionally selective constraints may impose on epigenetic evolution after gene duplication. Furthermore, duplicate genes with distinct functions have more divergence in histone modification compared with the ones with the same function, while higher expression divergence is found with mutations of chromatin modifiers. This study shows the role of epigenetic marks in regulating gene expression and functional divergence after gene duplication in plants based on sequencing data. creator: Jingjing Wang creator: Yuriy L. Orlov creator: Xue Li creator: Yincong Zhou creator: Yongjing Liu creator: Chunhui Yuan creator: Ming Chen uri: https://doi.org/10.7717/peerj.10426 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Wang et al. title: A new species of Munida Leach, 1820 (Crustacea: Decapoda: Anomura: Munididae) from seamounts of the Nazca-Desventuradas Marine Park link: https://peerj.com/articles/10531 last-modified: 2021-01-05 description: Munida diritas sp. nov. is described for the seamounts near Desventuradas Islands, in the intersection of the Salas & Gómez and Nazca Ridges, Chile. Specimens of the new species were collected in the summit (∼200 m depth) of one seamount and observed by ROV at two nearby ones. This species is characterized by the presence of distinct carinae on the thoracic sternites 6 and 7. Furthermore, it is not related with any species from the continental shelf nor the slope of America, while it is closely related to species of Munida from French Polynesia and the West-Pacific Ocean (i.e., M. ommata, M. psylla and M. rufiantennulata). In situ observations indicate that the species lives among the tentacles of ceriantarid anemones and preys on small crustaceans. The discovery of this new species adds to the knowledge of the highly endemic benthic fauna of seamounts of the newly created Nazca-Desventuradas Marine Park, emphasizing the relevance of this area for marine conservation. creator: María de los Ángeles Gallardo Salamanca creator: Enrique Macpherson creator: Jan M. Tapia Guerra creator: Cynthia M. Asorey creator: Javier Sellanes uri: https://doi.org/10.7717/peerj.10531 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Gallardo Salamanca et al. title: Aerosol optical depth (AOD): spatial and temporal variations and association with meteorological covariates in Taklimakan desert, China link: https://peerj.com/articles/10542 last-modified: 2021-01-05 description: Aerosol optical depth (AOD) is a key parameter that reflects aerosol characteristics. However, research on the AOD of dust aerosols and various environmental variables is scarce. Therefore, we conducted in-depth studies on the distributions and variations of AOD in the Taklimakan Desert and its margins, China. We examined the correlation characteristics between AOD and meteorological factors combined with satellite remote sensing detection methods using MCD19A2-MODIS AOD products (from 2000, 2005, 2010, and 2015), MOD13Q1-MODIS normalized difference vegetation index products, and meteorological data. We analyzed the temporal and spatial distributions of AOD, periodic change trends, and important impacts of meteorological factors on AOD in the Taklimakan Desert and its margins. To explore the relationships between desert aerosols and meteorological factors, a random forest model was used along with environmental variables to predict AOD and rank factor contributions. Results indicated that the monthly average AOD exhibited a clear unimodal curve that reached its maximum in April. The AOD values followed the order spring (0.28) > summer (0.27) > autumn (0.18) > winter (0.17). This seasonality is clear and can be related to the frequent sandstorms occurring in spring and early summer. Interannual AOD showed a gradually increasing trend to 2010 then large changes to 2015. AOD tends to increase from south to north. Based on the general trend, the maximum value of AOD is more dispersed and its low-value area is always stable. The climatic index that has the most significant effect on AOD is relative humidity. creator: Jinglong Li creator: Xiangyu Ge creator: Qing He creator: Alim Abbas uri: https://doi.org/10.7717/peerj.10542 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Determining the influencing factors of preferential flow in ground fissures for coal mine dump eco-engineering link: https://peerj.com/articles/10547 last-modified: 2021-01-05 description: Ground fissures (GF), appearing in front of dumps, are one of the most obvious and harmful geological hazards in coal mining areas. Studying preferential flow and its influencing factors in the ground fissures of dumps may provide basic scientific support for understanding the rapid movement of water and vegetation restoration and reconstruction in mining areas. Based on field surveys of ground fissures, three typical ground fissures were selected in the studied dump. The morphological characteristics of preferential flow for ground fissures were determined through field dye tracing, laboratory experiments, and image processing technology. The results indicated that the lengths of the three ground fissures ranged from 104.84 cm to 120.83 cm, and the widths ranged from 2.86 cm to 9.85 cm. All of the ground fissure area densities were less than 10%, and the proportion of ground fissure surface area was small in the dump. The maximum fissure depth was 47 cm, and the minimum was 16 cm. The ground fissure widths ranged from 0 cm to 14.98 cm, and the fissure width and fissure width-to-depth ratios decreased with increasing soil depth. The stained area was greater than 90% in the 0–5 cm soil layers of the three fissures, and water movement was dominated by matrix flow. The stained width decreased from 90 cm to 20 cm with increasing soil depth. The preferential flow was mainly concentrated on both sides of the fissure, which was distributed as a “T” shape. The preferential flow stained area ratios were 27.23%, 31.97%, and 30.73%, respectively, and these values decreased with increasing soil depth. The maximum stained depths of the preferential flow among the three fissures were different, and the maximum stained depth of GF II was significantly larger than that of GF I and GF III (P < 0.05). The stained path numbers of the three fissures ranged from 0 to 49. With increasing soil depth, the stained path number first increased and then decreased. The stained path widths of the three fissures ranged from 0 cm to 90 cm. With the increase in soil depth, the stained path width decreased. The stained area ratio was significantly positively correlated with ground fissure width, the ground fissure width-to-depth ratio, soil saturated hydraulic conductivity, soil organic matter, and sand content and was significantly negatively correlated with soil water content and clay content. The stained path number was significantly positively correlated with ground fissure width, the ground fissure width-to-depth ratio, soil saturated hydraulic conductivity and soil organic matter. The stained path width was significantly positively correlated with the ground fissure width-to-depth ratio, soil saturated hydraulic conductivity, soil organic matter and sand content and was significantly negatively correlated with clay content. Plant roots could significantly increase the stained area ratio, stained path number, and width and promote the formation and development of preferential flow. creator: Yexin Li creator: Gang Lv creator: Hongbo Shao creator: Quanhou Dai creator: Xinpeng Du creator: Dong Liang creator: Shaoping Kuang creator: Daohan Wang uri: https://doi.org/10.7717/peerj.10547 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Improving insect conservation across heterogeneous landscapes using species–habitat networks link: https://peerj.com/articles/10563 last-modified: 2021-01-05 description: BackgroundOne of the biggest challenges in conservation is to manage multiple habitats for the effective conservation of multiple species, especially when the focal species are mobile and use multiple resources across heterogeneous protected areas. The application of ecological network tools and the analysis of the resulting species–habitat networks can help to describe such complex spatial associations and improve the conservation of species at the landscape scale.MethodsTo exemplify the application of species–habitat networks, we present a case study on butterflies inhabiting multiple grassland types across a heterogeneous protected area in North-East Italy. We sampled adult butterflies in 44 sites, each belonging to one of the five major habitat types in the protected area, that is, disturbed grasslands, continuous grasslands, evolved grasslands, hay meadows and wet meadows. First, we applied traditional diversity analyses to explore butterfly species richness and evenness. Second, we built and analyzed both the unipartite network, linking habitat patches via shared species, and the bipartite network, linking species to individual habitat patches.Aims(i) To describe the emerging properties (connectance, modularity, nestedness, and robustness) of the species–habitat network at the scale of the whole protected area, and (ii) to identify the key habitats patches for butterfly conservation across the protected area, that is, those supporting the highest number of species and those with unique species assemblages (e.g., hosting specialist species).ResultsThe species–habitat network appeared to have a weak modular structure, meaning that the main habitat types tended to host different species assemblages. However, the habitats also shared a large proportion of species that were able to visit multiple habitats and use resources across the whole study area. Even butterfly species typically considered as habitat specialists were actually observed across multiple habitat patches, suggesting that protecting them only within their focal habitat might be ineffective. Our species–habitat network approach helped identifying both central habitat patches that were able to support the highest number of species, and habitat patches that supported rare specialist species. creator: Andree Cappellari creator: Lorenzo Marini uri: https://doi.org/10.7717/peerj.10563 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Cappellari and Marini title: Bacterial meta-analysis of chicken cecal microbiota link: https://peerj.com/articles/10571 last-modified: 2021-01-05 description: Poultry production is an industry that generates 90,000 metric tons of chicken meat worldwide. Thus, optimizing chicken growth and sustainable production is of great importance. A central factor determining not only production parameters, but also stability of the immune system and chicken health, is the diversity and variability of the microbiota present throughout the gastrointestinal tract. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on studies using amplicon sequencing with Illumina sequencing technologies in order to build a baseline for comparison in future analyses of the cecal bacterial composition in chicken. A systematic literature review was performed (SYRF ID: e84f0468-e418-4eec-9da4-b517f1b4809d. Full project URL: https://app.syrf.org.uk/projects/e84f0468-e418-4eec-9da4-b517f1b4809d/detail). From all the available and analyzed manuscripts only nine contained full raw-sequence data available and the corresponding metadata. A total of 324 samples, comprising three different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 11 phyla, with Firmicutes as the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 109 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. Despite the large number of parameters that were taken into account, the identification of common bacteria showed five genera to be common for all sets in at least 50% of the samples. These genera are highly associated to cellulose degradation and short chain fatty acids synthesis. In general, it was possible to identify some commonalities in the bacterial cecal microbial community despite the extensive variability and factors differing from one study to another. creator: Luis Alberto Chica Cardenas creator: Viviana Clavijo creator: Martha Vives creator: Alejandro Reyes uri: https://doi.org/10.7717/peerj.10571 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Chica Cardenas et al. title: Research on the measurement of intracranial hemorrhage in rabbits by a parallel-plate capacitor link: https://peerj.com/articles/10583 last-modified: 2021-01-05 description: Intracranial hemorrhage (ICH) carrying extremely high morbidity and mortality can only be detected by CT, MRI and other large equipment, which do not meet the requirements for bedside continuous monitoring and pre-hospital first aid. Since the biological tissues have different dielectric properties except the pure resistances, and the permittivity of blood is far larger than that of other brain tissues, here a new method was used to detect events of change at the blood/tissue volume ratio by measuring of the head permittivity. In this paper, we use a self-made parallel plate capacitor to detect the intracranial hemorrhage in rabbits by contactless capacitance measurement. The sensitivity of the parallel-plate capacitor was also evaluated by the physical solution measurement. The results of physical experiments show that the capacitor can distinguish between three solutions with different permittivity, and the capacitance increased with the increase of one solution between two plates. At the next step in the animal experiment, the capacitance changes caused by 2 ml blood injection into the rabbit brain were measured. The results of animal experiments show that the capacitance was almost unchanged before and after the blood injection, but increased with the increase of the blood injection volume. The increase of capacitance caused by blood injection was much larger than that before and after blood injection (P < 0.01). The experiments show that this method is feasible for the detection of intracranial hemorrhage in a non-invasive and contactless manner. creator: Zelin Bai creator: Haocheng Li creator: Jingbo Chen creator: Wei Zhuang creator: Gen Li creator: Mingsheng Chen creator: Jia Xu creator: Shuanglin Zhao creator: Yuening Liu creator: Jian Sun creator: Feng Wang creator: Lin Xu creator: Mingxin Qin creator: Gui Jin uri: https://doi.org/10.7717/peerj.10583 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Bai et al. title: Lead transfer in the soil-root-plant system in a highly contaminated Andean area link: https://peerj.com/articles/10624 last-modified: 2021-01-05 description: Lead (Pb) is highly toxic heavy metal that is detrimental to the food system. There are large mining and metallurgical companies in the central highlands of Peru that have been active for almost a century and contribute to air, water, and soil pollution, affecting food quality and causing damage to the environment and human health. Our study, conducted in 2018, assessed the content and transfer of lead in the soil-root-plant system in the high Andean grasslands in a geographical area near the metallurgical complex of La Oroya. Lead levels were measured in 120 samples of top soil (0–20 cm), roots, and grass shoots by flame atomic absorption spectroscopy. No significant differences were found between the soil pH, organic matter content, and lead among the samples evaluated (P > 0.05). Mean Pb concentrations decreased in the order of soil > root > shoot (P < 0.01) (212.36 ±  38.40, 154.65 ±  52.85 and 19.71 ±  2.81 mg/kg, respectively). The soil-to-root Pb bioconcentration factor, root-to-shoot translocation factor, and soil-to-shoot bioaccumulation factor values were 0.74 ±  0.26, 0.14 ±  0.06 and 0.10 ±  0.03, respectively. Lead in the soil was 3.03 times higher than the maximum limit for agricultural soil, and was 1.97 times higher than the value limit for fodder. Our findings are important and show that soils and pasture in this geographical area have high Pb levels due to metallurgical emissions that have been occurring since 1922. Such pollution negatively impacts health and the socio-economic status of the exposed populations. creator: Jorge Castro-Bedriñana creator: Doris Chirinos-Peinado creator: Edgar Garcia-Olarte creator: Rolando Quispe-Ramos uri: https://doi.org/10.7717/peerj.10624 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Castro-Bedriñana et al. title: Measurement and differentiation of banana juice scent using an electronic nose FF-2A link: https://peerj.com/articles/10638 last-modified: 2021-01-05 description: BackgroundBanana juice is becoming a popular beverage in Japan and the number of soft-drink stands or shops that take great care and pride in the quality of their products has been increasing. This study aims to measure the scent of banana juice from different brands using the electronic (e-) nose FF-2A in order to identify the characteristics, time-related changes, and the differences among them.MethodsWe standardized the scent value of banana juice measured using FF-2A and determined the absolute value in three different shops. We compared the similarities in samples from each shop with axis data created using standardized measurement. With FF-2A we identified the scent common to all banana juice samples from the composite scent and numerically showed the similarity to the reference gas.ResultsThe juices from each shop had their own characteristics and we were able to identify the difference between some of these. The response of FF-2A varied according to the increase/decrease in the number of characteristic molecules measured by GC-MS such as overtime fluctuations in the gas. These data were shown along with the differences between the various banana juices.ConclusionsFF-2A was able to identify the scent of banana juice at each banana shop as well as time-related changes. By combining GC-MS, we were able to evaluate scent components that changed over time. The results using the electronic nose may prove useful for objective evaluation and comparison of scent with other types of juices. creator: Mayumi Nomura creator: Erika Osada creator: Tsuyoshi Tokita creator: Takeo Iwamoto creator: Yoshinobu Manome uri: https://doi.org/10.7717/peerj.10638 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Nomura et al. title: Grazer density and songbird counts in a restored conservation area link: https://peerj.com/articles/10657 last-modified: 2021-01-05 description: Grazing by large herbivores is increasingly used as a management tool in European nature reserves. The aim is usually to support an open but heterogeneous habitat and its corresponding plant and animal communities. Previous studies showed that birds may profit from grazing but that the effect varies among bird species. Such studies often compared bird counts among grazed areas with different stocking rates of herbivores. Here, we investigated how space use of Konik horses and Highland cattle is related to bird counts in a recently restored conservation area with a year-round natural grazing management. We equipped five horses and five cattle with GPS collars and correlated the density of their GPS positions on the grazed area with the density of bird observations from winter through the breeding season. We found that in the songbirds of our study site, both the overall density of bird individuals and the number of species increased with increasing density of GPS positions of grazers. Correlations of bird density with horse density were similar to correlations with cattle density. Of the eight most common songbird species observed in our study area, the Eurasian Skylark and the Common Starling had the clearest positive correlations with grazer density, while the Blackbird showed a negative correlation. Skylarks and Starlings in our study area thus seem to profit from year-round natural grazing by a mixed group of horses and cattle. creator: Lilla Lovász creator: Fränzi Korner-Nievergelt creator: Valentin Amrhein uri: https://doi.org/10.7717/peerj.10657 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Lovász et al.