title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=635 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Proteomic response of early juvenile Pacific oysters (Crassostrea gigas) to temperature link: https://peerj.com/articles/14158 last-modified: 2022-10-14 description: Pacific oysters (Crassostrea gigas) are a valuable aquaculture product that provides important ecosystem benefits. Among other threats, climate-driven changes in ocean temperature can impact oyster metabolism, survivorship, and immune function. We investigated how elevated temperature impacts larval oysters during settlement (19–33 days post-fertilization), using shotgun proteomics with data-independent acquisition to identify proteins present in the oysters after 2 weeks of exposure to 23 °C or 29 °C. Oysters maintained at elevated temperatures were larger and had a higher settlement rate, with 86% surviving to the end of the experiment; these oysters also had higher abundance trends of proteins related to metabolism and growth. Oysters held at 23 °C were smaller, had a decreased settlement rate, displayed 100% mortality, and had elevated abundance trends of proteins related to immune response. This novel use of proteomics was able to capture characteristic shifts in protein abundance that hint at important differences in the phenotypic response of Pacific oysters to temperature regimes. Additionally, this work has produced a robust proteomic product that will be the basis for future research on bivalve developmental processes. creator: Grace Crandall creator: Rhonda Elliott Thompson creator: Benoit Eudeline creator: Brent Vadopalas creator: Emma Timmins-Schiffman creator: Steven Roberts uri: https://doi.org/10.7717/peerj.14158 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Crandall et al. title: The mechanism analysis of exogenous melatonin in limiting pear fruit aroma decrease under low temperature storage link: https://peerj.com/articles/14166 last-modified: 2022-10-14 description: Exogenous melatonin (MT) is widely used in fruit preservation, and can increase the storage time and delay the quality deterioration. Firstly, it was found that 150 μM MT was the optimal concentration to treat ‘Xinli No.7’ under storage at 4 °C for 60 days. MT could significantly improve oxidase activity and inhibit the reduction of physiological indexes, including pulp hardness, weight loss, titratable acid and soluble solid content. MT could also reduce ethylene release and limit the reduction of fruit aroma. The average content of fruit aroma substance increased by 43.53%. A relevant RNA-Seq database was built to further explore the regulation mechanism of MT. A total of 2,761 differentially expressed genes (DEGs) were identified. DEGs were enriched in 64 functional groups and 191 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. DEGs were mainly enriched in alpha-linolenic acid metabolism, fatty acid metabolism and plant hormone signal transduction pathway. The gene pycom09g05270 belonging to long chain acyl-CoA synthetase family and participating in fatty acid metabolism pathway was identified, and its expression level was consistent with fragments per kilobase per million mapped reads (FPKM) values, implying that pycom09g05270 might play a vital role in maintaining quality during the storage process. creator: Shuwei Wei creator: Huijun Jiao creator: Hongwei Wang creator: Kun Ran creator: Ran Dong creator: Xiaochang Dong creator: Wenjing Yan creator: Shaomin Wang uri: https://doi.org/10.7717/peerj.14166 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wei et al. title: Genetic species identification and population structure of grouper Epinephelus coioides (Hamilton, 1822) collected from fish markets along the Persian Gulf and the Oman Sea link: https://peerj.com/articles/14179 last-modified: 2022-10-14 description: Many ecologically important and valuable fisheries marine species have been misidentified in terms of both the statistical data and market demand. Correct identification at the species level and the population genetic structure of the orange-spotted grouper (Epinephelus coioides), a precious fish in the Persian Gulf and the Oman Sea, was tested using mitochondrial cytochrome oxidase subunit I (DNA barcoding) and D-loop sequencing. The results revealed that the Epinephelus species found in the region, including E. coioides, E. bleekeri, E. polylepis, and E. chlorostigma were all mistakenly grouped together and identified as only E. coioides. Moreover, the analysis of molecular variance (AMOVA) of E. coioides samples using the D-loop showed a significantly unique genetic structure (ΦST = 0.068, p < 0.001) within the E. coioides population throughout the Persian Gulf and the Oman Sea, with the pairwise genetic difference between sampling locations in UAE and the Iranian coast. Moreover, D-loop sequences analysis showed two distinct haplotype groups scattered among the sampling locations, which did not correlate with the geographic distance between the sampling locations. These findings indicate that the issue of misidentification should be highlighted in the management and conservation of E. coioides. As this type of misidentification is likely to happen to other threatened marine species as well, the efficacy of using genetic markers for the correct identification, both at the species and the population level, is vital. creator: Parviz Tavakoli-Kolour creator: Ahmad Farhadi creator: Ashkan Ajdari creator: Dara Bagheri creator: Sanaz Hazraty-Kari creator: Ahmad Ghasemi creator: Arya Vazirzadeh uri: https://doi.org/10.7717/peerj.14179 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Tavakoli-Kolour et al. title: biomonitoR: an R package for managing ecological data and calculating biomonitoring indices link: https://peerj.com/articles/14183 last-modified: 2022-10-14 description: The monitoring of biological indicators is required to assess the impacts of environmental policies, compare ecosystems and guide management and conservation actions. However, the growing availability of ecological data has not been accompanied by concomitant processing tools able to facilitate data handling and analysis. Multiple common challenges limit the usefulness of biomonitoring information across ecosystems and biological groups. Biomonitoring data analysis is currently constrained by time-consuming steps for data preparation and a data processing environment with limited integration in terms of software, biological groups, and protocols. We introduce biomonitoR, a package for the R programming language that addresses technical challenges for the management of ecological data and metrics calculation. biomonitoR implements most of the biological indices currently used or proposed in different fields of ecology and water resource management. Its combination of customizable functions aims to support a transferable and comprehensive biomonitoring workflow in a user-friendly environment. biomonitoR represents a versatile toolbox with five main assets: (i) it checks taxonomic information against reference datasets allowing for customization of trait and sensitivity scores; (ii) it supports heterogeneous taxonomic resolution allowing computations at multiple taxonomic levels; (iii) it calculates multiple biological indices, including metrics for both broad and stressor-specific ecological assessments; (iv) it enables user-friendly data visualization, helping both decision-making processes and data interpretation; and (v) it allows working with an interactive web application straight from R. Overall, biomonitoR can benefit the wide biomonitoring community, including environmental private consultants, ecologists and natural resource managers. creator: Alex Laini creator: Simone Guareschi creator: Rossano Bolpagni creator: Gemma Burgazzi creator: Daniel Bruno creator: Cayetano Gutiérrez-Cánovas creator: Rafael Miranda creator: Cédric Mondy creator: Gábor Várbíró creator: Tommaso Cancellario uri: https://doi.org/10.7717/peerj.14183 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Laini et al. title: RFfiller: a robust and fast statistical algorithm for gap filling in draft genomes link: https://peerj.com/articles/14186 last-modified: 2022-10-14 description: Numerous published genomes contain gaps or unknown sequences. Gap filling is a critical final step in de novo genome assembly, particularly for large genomes. While certain computational approaches partially address the problem, others have shortcomings regarding the draft genome’s dependability and correctness (high rates of mis-assembly at gap-closing sites and high error rates). While it is well established that genomic repeats result in gaps, many sequence reads originating from repeat-related gaps are typically missed by existing approaches. A fast and reliable statistical algorithm for closing gaps in a draft genome is presented in this paper. It utilizes the alignment statistics between scaffolds, contigs, and paired-end reads to generate a Markov chain that appropriately assigns contigs or long reads to scaffold gap regions (only corrects candidate regions), resulting in accurate and efficient gap closure. To reconstruct the missing component between the two ends of the same insert, the RFfiller meticulously searches for valid overlaps (in repeat regions) and generates transition tables for similar reads, allowing it to make a statistical guess at the missing sequence. Finally, in our experiments, we show that the RFfiller’s gap-closing accuracy is better than that of other publicly available tools when sequence data from various organisms are used. Assembly benchmarks were used to validate RFfiller. Our findings show that RFfiller efficiently fills gaps and that it is especially effective when the gap length is longer. We also show that the RFfiller outperforms other gap closing tools currently on the market. creator: Firaol Dida Midekso creator: Gangman Yi uri: https://doi.org/10.7717/peerj.14186 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Midekso and Yi title: Automated mapping of Portulacaria afra canopies for restoration monitoring with convolutional neural networks and heterogeneous unmanned aerial vehicle imagery link: https://peerj.com/articles/14219 last-modified: 2022-10-14 description: Ecosystem restoration and reforestation often operate at large scales, whereas monitoring practices are usually limited to spatially restricted field measurements that are (i) time- and labour-intensive, and (ii) unable to accurately quantify restoration success over hundreds to thousands of hectares. Recent advances in remote sensing technologies paired with deep learning algorithms provide an unprecedented opportunity for monitoring changes in vegetation cover at spatial and temporal scales. Such data can feed directly into adaptive management practices and provide insights into restoration and regeneration dynamics. Here, we demonstrate that convolutional neural network (CNN) segmentation algorithms can accurately classify the canopy cover of Portulacaria afra Jacq. in imagery acquired using different models of unoccupied aerial vehicles (UAVs) and under variable light intensities. Portulacaria afra is the target species for the restoration of Albany Subtropical Thicket vegetation, endemic to South Africa, where canopy cover is challenging to measure due to the dense, tangled structure of this vegetation. The automated classification strategy presented here is widely transferable to restoration monitoring as its application does not require any knowledge of the CNN model or specialist training, and can be applied to imagery generated by a range of UAV models. This will reduce the sampling effort required to track restoration trajectories in space and time, contributing to more effective management of restoration sites, and promoting collaboration between scientists, practitioners and landowners. creator: Nicholas C. Galuszynski creator: Robbert Duker creator: Alastair J. Potts creator: Teja Kattenborn uri: https://doi.org/10.7717/peerj.14219 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Galuszynski et al. title: Coral reef fish assemblages exhibit signs of depletion in two protected areas from the eastern of Los Canarreos archipelago (Cuba, Caribbean Sea) link: https://peerj.com/articles/14229 last-modified: 2022-10-14 description: Understanding the impact of marine protected areas on the distribution and composition of fishes is key to the protection and management of coral reef ecosystems, and especially for fish-based activities such as SCUBA diving and recreational fishing. The aim of this research is to compare the ichthyofauna structure in three areas in the eastern part of Los Canarreos archipelago in Cuba with different management schemes: Cayo Campos-Cayo Rosario Fauna Refuge (CCCR), Cayo Largo Ecological Reserve (CL) and non-protected area (nMPA), and considering habitat differences and depth variation. A total of 131 video transects were conducted using diver operated stereo-video (stereo-DOV) in November, 2015 in backreef and forereef along the CCCR, CL and the adjacent nMPA. We recorded 84 species and 27 functional groups suggesting high complementarity of functions. Several multispecies schools were observed along surveys, which explain the biomass peaks in some sites, mainly for Lutjanidae, Haemulidae and Carangidae. A concerning issue was the bare representation of critical functional groups and threatened species. The effect of sites nested within habitats was significant and the most important driver structuring fish assemblages, while MPA condition was not evident. Favorable habitat features (habitat heterogeneity and surrounding coastal ecosystems) are likely enhancing fish assemblages and counteracting the effects of pouching derived from insufficient management. We recommend immediate actions within a strategy of precautionary management including, but not limited to, the appointment of staff for the administration of CL, frequent monitoring and effective enforcement. creator: Zenaida María Navarro-Martínez creator: Maickel Armenteros creator: Leonardo Espinosa creator: Patricia González-Díaz creator: Amy Apprill uri: https://doi.org/10.7717/peerj.14229 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Navarro-Martínez et al. title: Postpartum depression and health-related quality of life: a Saudi Arabian perspective link: https://peerj.com/articles/14240 last-modified: 2022-10-14 description: Background and ObjectivesThe mental and physical functioning of an individual is partly determined by their health-related quality of life (HRQOL), which is a multifaceted component. Women who have recently given birth must have a good quality of life to provide proper care and development for their infant. The purpose of this study was to assess the relationship between postpartum depression (PPD) and HRQOL in Saudi Arabian women and to identify potential risk factors that could influence them.MethodsThis study comprised 253 mothers aged 1–24 weeks postpartum from several health centers in Saudi Arabia, recruited by random purposive sampling. The study’s questionnaire featured three sections: the first section had demographic information; the second and third sections contained the Edinburgh Postnatal Depression Scale (EPDS) scale and the HRQOL scale (SF-12), respectively. Data were analyzed using descriptive statistics, chi square analyses, independent samples t-tests and binary logistic regression analysis using IBM SPSS 25.ResultsResults of current study indicate that 59.68% of the patients exhibited probable post-partum depression symptoms. Participants who were depressed had significantly lower mental component (MCS) and physical component scores than participants who were in good health. When compared to non-smokers, smokers have a 21-fold higher risk of developing depression. Similar to this, mothers who worked had a 3.98 times higher risk of depression, and patients with a history of depression had a 3.6 times higher chance of getting PPD. The probability of developing PPD was also significantly higher in those who lived outside the Riyadh region, had given birth more than twice before this time, and had experienced undesired pregnancies.ConclusionOur study demonstrated an inverse correlation between postpartum depression and health-related quality of life scores. Treatment for depression, particularly among mothers, is crucial for improving their quality of life and, as a result, creating a favorable environment for the development of newborn babies. creator: Mansour Almuqbil creator: Nora Kraidiye creator: Hatoun Alshmaimri creator: Amerah Ali kaabi creator: Atheer Almutiri creator: Abeer Alanazi creator: Ayat Hjeij creator: Abdulhakeem S. Alamri creator: Wala F. Alsanie creator: Majid Alhomrani creator: Syed Mohammed Basheeruddin Asdaq uri: https://doi.org/10.7717/peerj.14240 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Almuqbil et al. title: Ribovirus classification by a polymerase barcode sequence link: https://peerj.com/articles/14055 last-modified: 2022-10-13 description: RNA viruses encoding a polymerase gene (riboviruses) dominate the known eukaryotic virome. High-throughput sequencing is revealing a wealth of new riboviruses known only from sequence, precluding classification by traditional taxonomic methods. Sequence classification is often based on polymerase sequences, but standardised methods to support this approach are currently lacking. To address this need, we describe the polymerase palmprint, a segment of the palm sub-domain robustly delineated by well-conserved catalytic motifs. We present an algorithm, Palmscan, which identifies palmprints in nucleotide and amino acid sequences; PALMdb, a collection of palmprints derived from public sequence databases; and palmID, a public website implementing palmprint identification, search, and annotation. Together, these methods demonstrate a proof-of-concept workflow for high-throughput characterisation of RNA viruses, paving the path for the continued rapid growth in RNA virus discovery anticipated in the coming decade. creator: Artem Babaian creator: Robert Edgar uri: https://doi.org/10.7717/peerj.14055 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Babaian and Edgar title: Planting Cyperus esculentus augments soil microbial biomass and diversity, but not enzymatic activities link: https://peerj.com/articles/14199 last-modified: 2022-10-13 description: The planting of Cyperus esculentus, a member of the grass family Cyperaceae which includes nut sedge weeds, is being increasingly promoted in northern China’s semi-arid and arid regions. Yet the effects of planting C. esculentus upon soil quality and soil microbial characteristics of sandy land remain unclear. This study examined the short-term (1 year) impact of this grass species on soil microbial biomass indices, enzymatic activities, and microbiome characteristics in the Horqin Sandy Land area of China. The results show that planting C. esculentus could increase microbial biomass in the form of carbon (MBC), nitrogen (MBN), and phosphorus (MBP), but it negligibly influenced the enzymatic activities of soil β-1,4-glucosidase (BG), cellobiohydrolase (CBH), leucine aminopeptidase (LAP), and β-1,4-N-acetaminoglycosidase (NAG). Over 1 year, we found that planting C. esculentus significantly increased the soil bacterial richness and diversity of sandy land, yet also altered community composition of soil bacteria and eukaryotes in way that could promote their homogenization. In this respect, the relative abundances of Acidobacteria and Proteobacteria significantly decreased and increased, respectively; hence, they may be considered for use as important indicators of soil nutrient-rich conditions. Overall, the results could be explained by greater soil organic carbon (SOC) and total nitrogen (TN), mainly derived from cumulative plant litter input to soils, which then increased the sandy soil’s C:N ratio. Future research should focus on exploring the long-term effects of planting C. esculentus on soil quality and soil microbial characteristics of sandy lands in China and abroad. creator: Yulong Duan creator: Wei Ren creator: Jianhua Zhao creator: Chun Luo creator: Yang Liu uri: https://doi.org/10.7717/peerj.14199 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2022 Duan et al.