title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=646 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Influence of planting yellowhorn (Xanthoceras sorbifolium Bunge) on the bacterial and fungal diversity of fly ash link: https://peerj.com/articles/14015 last-modified: 2022-09-23 description: Phytoremediation is a low-cost solution to fly ash pollution and the rhizosphere interactions between plant roots and the fly ash microbiome were important for the phytoremediation. To analyze the dynamic changes of the rhizosphere microbiome during yellowhorn cultivation in fly ash, the bacterial 16S rRNA gene V3–V4 region and the fungal ITS region of the rhizosphere microbiome were sequenced using Illumina MiSeq technology. The changes in fly ash physicochemical properties and the heavy metal content of different yellowhorn tissues were also analyzed. The results showed that both the bacterial and fungal communities were noticeably different after yellowhorn cultivation compared with the control sample. Proteobacteria and Acidobacteria levels increased (p < 0.05) and Firmicutes and Actinobacteria decreased (p < 0.05) in the bacterial community after yellowhorn cultivation. In the fungal community, Ascomycota and Mortierellomycota decreased (p < 0.05), while Chytridiomycota increased (p < 0.05). The levels of four heavy metals (Cr, Cd, Hg, Pb and As) decreased in the fly ash after yellowhorn cultivation. These metals were absorbed by the yellowhorn plants and accumulated in the fibrous root, taproot, stem and leaf tissues of these plants. Accordingly, the abundance of bacteria that could solubilize heavy metals increased (p < 0.05). In summary, the cultivation of yellowhorn affected the composition of the rhizosphere microbial communities in fly ash, which is of great significance for the biological remediation of fly ash. creator: Zehui Liu creator: Jianguo Zhao creator: Jinxian Huo creator: Hongfang Ma creator: Zhiwen Chen uri: https://doi.org/10.7717/peerj.14015 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Liu et al. title: Analysis of inferior nasal turbinate volume in subjects with nasal septum deviation: a retrospective cone beam tomography study link: https://peerj.com/articles/14032 last-modified: 2022-09-23 description: BackgroundThe association of the linear dimensions of the inferior turbinate hypertrophy with nasal septal deviation has been studied recently. However, the volumetric dimensions provide a more accurate status of the turbinate hypertrophy compared to linear measurements. The aim of this study was to analyze the association of inferior nasal turbinate volume with the degree of nasal septal deviation (NSD).MethodsA retrospective evaluation of the cone beam computed tomography (CBCT) scans of 412 patients was carried out to obtain 150 scans which were included in the study. The scans were categorized into three groups. Group 1 comprised of 50 scans of patients with no inferior turbinate hypertrophy (ITH) and no nasal septal deviation. Group 2 comprised of 50 scans of patients with ITH and no NSD; whereas Group 3 included 50 scans of patients with ITH and NSD. The total turbinate volume of inferior turbinates (bilateral) were determined by using Vesalius 3D software (PS-Medtech, Amsterdam, Netherlands).ResultsThe intraclass correlation coefficient (ICC) between the volumetric estimations performed by the two radiologists was 0.82. There were no significant age and gender related changes in the total turbinate volume. Patients in Group 3 had significantly higher (p = 0.001) total turbinate volume compared to Group 2 and Group 1. There was a positive and significant correlation (r = 0.52, p = 0.002) between the degree of septal deviation and total turbinate volume. When the total turbinate volume of the patients with different types of septal deviation was compared in Group 3, a statistically significant difference (p = 0.001) was observed. Regression analysis revealed that the septal deviation angle (SDA) (p = 0.001) had a relationship with total turbinate volume. From the results of the study we can conclude that the total turbinate volume is higher in patients with nasal septal deviation. It can also be concluded that the septal deviation angle has a positive correlation with total turbinate volume. The data obtained from the study can be useful in post-surgical follow up and evaluation of patients with nasal septal deviation and hypertrophied inferior nasal turbinate. creator: Shishir Shetty creator: Saad Al-Bayatti creator: Mohammad Khursheed Alam creator: Natheer H. Al-Rawi creator: Vinayak Kamath creator: Shoaib Rahman Tippu creator: Sangeetha Narasimhan creator: Sausan Al Kawas creator: Walid Elsayed creator: Kumuda Rao creator: Renita Castelino uri: https://doi.org/10.7717/peerj.14032 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Shetty et al. title: Dental caries as a risk factor for bacterial blood stream infection (BSI) in children undergoing hematopoietic cell transplantation (HCT) link: https://peerj.com/articles/14040 last-modified: 2022-09-23 description: BackgroundHematopoietic cell transplantation (HCT) is a potentially curative therapy for a wide range of pediatric malignant and nonmalignant diseases. However, complications, including blood stream infection (BSI) remain a major cause of morbidity and mortality. While certain bacteria that are abundant in the oral microbiome, such as S. mitis, can cause BSI, the role of the oral microbial community in the etiology of BSI is not well understood. The finding that the use of xylitol wipes, which specifically targets the cariogenic bacteria S. mutans is associated with reduced BSI in pediatric patients, lead us to investigate dental caries as a risk factor for BSI.MethodsA total of 41 pediatric patients admitted for allogenic or autologous HCT, age 8 months to 25 years, were enrolled. Subjects with high dental caries risk were identified as those who had dental restorations completed within 2 months of admission for transplant, or who had untreated decay. Fisher’s exact test was used to determine if there was a significant association between caries risk and BSI. Dental plaque and saliva were collected on a cotton swab from a subset of four high caries risk (HCR) and four low caries risk (LCR) children following pretransplant conditioning. 16SrRNA sequencing was used to compare the microbiome of HCR and LCR subjects and to identify microbes that were significantly different between the two groups.ResultsThere was a statistically significant association between caries risk and BSI (p < 0.035) (Fisher’s exact test). Multivariate logistic regression analysis showed children in the high dental caries risk group were 21 times more likely to have BSI, with no significant effect of age or mucositis severity. HCR subjects showed significantly reduced microbial alpha diversity as compared to LCR subjects. LEfse metagenomic analyses, showed the oral microbiome in HCR children enriched in order Lactobacillales. This order includes Streptococcus and Lactobacillus, both which contain bacteria primarily associated with dental caries.DiscussionThese findings support the possibility that the cariogenic microbiome can enhance the risk of BSI in pediatric populations. Future metagenomic analyses to measure microbial differences at, before, and after conditioning related to caries risk, may further unravel the complex relationship between the oral microbiome, and whether it affects health outcomes such as BSI. creator: Dawud Abduweli Uyghurturk creator: Ying Lu creator: Janelle Urata creator: Christopher C. Dvorak creator: Pamela Den Besten uri: https://doi.org/10.7717/peerj.14040 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 abduweli uyghurturk et al. title: 16S-FASAS: an integrated pipeline for synthetic full-length 16S rRNA gene sequencing data analysis link: https://peerj.com/articles/14043 last-modified: 2022-09-23 description: BackgroundThe full-length 16S rRNA sequencing can better improve the taxonomic and phylogenetic resolution compared to the partial 16S rRNA gene sequencing. The 16S-FAS-NGS (16S rRNA full-length amplicon sequencing based on a next-generation sequencing platform) technology can generate high-quality, full-length 16S rRNA gene sequences using short-read sequencers, together with assembly procedures. However there is a lack of a data analysis suite that can help process and analyze the synthetic long read data.ResultsHerein, we developed software named 16S-FASAS (16S full-length amplicon sequencing data analysis software) for 16S-FAS-NGS data analysis, which provided high-fidelity species-level microbiome data. 16S-FASAS consists of data quality control, de novo assembly, annotation, and visualization modules. We verified the performance of 16S-FASAS on both mock and fecal samples. In mock communities, we proved that taxonomy assignment by MegaBLAST had fewer misclassifications and tended to find more low abundance species than the USEARCH-UNOISE3-based classifier, resulting in species-level classification of 85.71% (6/7), 85.71% (6/7), 72.72% (8/11), and 70% (7/10) of the target bacteria. When applied to fecal samples, we found that the 16S-FAS-NGS datasets generated contigs grouped into 60 and 56 species, from which 71.62% (43/60) and 76.79% (43/56) were shared with the Pacbio datasets.Conclusions16S-FASAS is a valuable tool that helps researchers process and interpret the results of full-length 16S rRNA gene sequencing. Depending on the full-length amplicon sequencing technology, the 16S-FASAS pipeline enables a more accurate report on the bacterial complexity of microbiome samples. 16S-FASAS is freely available for use at https://github.com/capitalbio-bioinfo/FASAS. creator: Ke Zhang creator: Rongnan Lin creator: Yujun Chang creator: Qing Zhou creator: Zhi Zhang uri: https://doi.org/10.7717/peerj.14043 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Clinical tool to measure fluorescein patterns in orthokeratology link: https://peerj.com/articles/14068 last-modified: 2022-09-23 description: BackgroundOrthokeratology (ortho-k) is an overnight clinical contact lens wear technique to correct myopia and to reduce myopia progression wearing reverse-geometry rigid gas-permeable lenses. The lens fitting procedure in clinical practice usually requires subjective assessment of fluorescein pattern (fluorescein “bull’s eye” pattern). The aim of this study was to develop a novel tool for fluorescein pattern measurements to reduce subjective practitioner dependency, especially in inexperienced practitioners, in ortho-k practice.MethodsA new MATLAB customized algorithm to measure the horizontal width of the four main zones of ortho-k fluorescein patterns (central bearing, tear reservoir, mid-peripheral bearing and edge lift) was designed. The algorithm was tested on a small image database consisting of 26 ortho-k fluorescein pattern images of 13 volunteers fitted with reverse geometry lenses (Seefree, Conoptica-Hecht Contactlinsen). The agreement between two independent observers and the ImageJ measurements was determined.ResultsThe new clinical tool provided similar measurements to ImageJ software for the central bearing (4.20 ± 0.74 and 4.27 ± 0.69 mm; P = 0.21), tear reservoir (1.69 ± 0.41 and 1.69 ± 0.45 mm; P = 0.69), mid-peripheral bearing (1.17 ± 0.11 and 1.13 ± 0.10 mm; P < 0.01) and edge lift (0.48 ± 0.06 and 0.48 ± 0.06 mm; P = 0.81) zones. Good agreement between the software (limits of agreement lower than ±0.55 mm) and inter-observer measurements (limits of agreement lower than ±0.66 mm) was found.ConclusionsThe proposed clinical tool for semiautomatic fluorescein pattern measurements in ortho-k could help to reduce practitioner dependency in fluorescein pattern assessment with future potential to introduce prediction algorithms or artificial intelligence methods in myopia control management. creator: Marina López García Rosuero creator: Alejandro Arranz Bombin creator: Roberto Romero creator: Roberto Hornero creator: Raul Martin uri: https://doi.org/10.7717/peerj.14068 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 López García Rosuero et al. title: BMSC-derived exosomal miR-27a-3p and miR-196b-5p regulate bone remodeling in ovariectomized rats link: https://peerj.com/articles/13744 last-modified: 2022-09-22 description: BackgroundIn the bone marrow microenvironment of postmenopausal osteoporosis (PMOP), bone marrow mesenchymal stem cell (BMSC)-derived exosomal miRNAs play an important role in bone formation and bone resorption, although the pathogenesis has yet to be clarified.MethodsBMSC-derived exosomes from ovariectomized rats (OVX-Exo) and sham-operated rats (Sham-Exo) were co-cultured with bone marrow-derived macrophages to study their effects on osteoclast differentiation. Next-generation sequencing was utilized to identify the differentially expressed miRNAs (DE-miRNAs) between OVX-Exo and Sham-Exo, while target genes were analyzed using bioinformatics. The regulatory effects of miR-27a-3p and miR-196b-5p on osteogenic differentiation of BMSCs and osteoclast differentiation were verified by gain-of-function and loss-of-function analyses.ResultsOsteoclast differentiation was significantly enhanced in the OVX-Exo treatment group compared to the Sham-Exo group. Twenty DE-miRNAs were identified between OVX-Exo and Sham-Exo, among which miR-27a-3p and miR-196b-5p promoted the expressions of osteogenic differentiation markers in BMSCs. In contrast, knockdown of miR-27a-3p and miR-196b-5p increased the expressions of osteoclastic markers in osteoclast. These 20 DE-miRNAs were found to target 11435 mRNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that these target genes were involved in several biological processes and osteoporosis-related signaling pathways.ConclusionBMSC-derived exosomal miR-27a-3p and miR-196b-5p may play a positive regulatory role in bone remodeling. creator: Guohua Lai creator: Renli Zhao creator: Weida Zhuang creator: Zuoxu Hou creator: Zefeng Yang creator: Peipei He creator: Jiachang Wu creator: Hongxun Sang uri: https://doi.org/10.7717/peerj.13744 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lai et al. title: Comparative analysis of combined phosphorus and drought stress-responses in two winter wheat link: https://peerj.com/articles/13887 last-modified: 2022-09-22 description: Phosphorus stress and drought stress are common abiotic stresses for wheat. In this study, two winter wheat varieties “Xindong20” and “Xindong23” were cultured in a hydroponic system using Hoagland nutrient solution and treated with drought stress under conventional (CP: 1.0 mmol/L) and low (LP: 0.05 mmol/L) phosphorus levels. Under drought stress, the root growth was better under LP than under CP. Under LP, root phosphorus content was increased by 94.2% in Xindong20 and decreased by 48.9% in Xindong23 at 3 d after re-watering, compared with those at 0 d under drought stress. However, the potassium (K) content was the highest among the four elements studied and the phosphorus (P) and calcium (Ca) content were reduced in the root of the two varieties. Under CP, the zinc (Zn) content was higher than that under LP in Xindong23. The GeneChip analysis showed that a total of 4,577 and 202 differentially expressed genes (DEGs) were detected from the roots of Xindong20 and Xindong23, respectively. Among them, 89.9% of DEGs were involved in organelles and vesicles in Xindong20, and 69.8% were involved in root anatomical structure, respiratory chain, electron transport chain, ion transport, and enzyme activity in Xindong23. Overall, LP was superior to CP in mitigating drought stress on wheat, and the regulatory genes were also different in the two varieties. Xindong20 had higher drought tolerance for more up-regulated genes involved in the responses compared to Xindong23. creator: Xiangchi Zhang creator: Chao Li creator: Weidan Lu creator: Xiaoli Wang creator: Bin Ma creator: Kaiyong Fu creator: Chunyan Li creator: Cheng Li uri: https://doi.org/10.7717/peerj.13887 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhang et al. title: Population dynamics and resource availability drive seasonal shifts in the consumptive and competitive impacts of introduced house mice (Mus musculus) on an island ecosystem link: https://peerj.com/articles/13904 last-modified: 2022-09-22 description: BackgroundHouse mice (Mus musculus) are widespread and invasive on many islands where they can have both direct and indirect impacts on native ecological communities. Given their opportunistic, omnivorous nature the consumptive and competitive impacts of house mice on islands have the potential to vary over time in concert with resource availability and mouse population dynamics.MethodsWe examined the ecological niche of invasive house mice on Southeast Farallon Island, California, USA using a combination of mouse trapping, food resource surveys, and stable isotope analysis to better understand their trophic interactions with native flora and fauna. Specifically, we coupled the analysis of seasonal variation in resource availability over a 17-year period (2001–2017), carbon (δ13C) and nitrogen (δ15N) stable isotope values of mouse tissue and prey resources in a single year (2013), and isotopic niche and mixing models to quantify seasonal variation in mouse diets and the potential for resource overlap with native species.ResultsWe found that plants were the most important resource for house mice during the spring months when vegetation is abundant and mouse populations are low following heavy precipitation and declines in mouse abundance during the winter. While still consumed, plants declined in dietary importance throughout the summer and fall as mouse populations increased, and seabird and arthropod resources became relatively more available and consumed by house mice. Mouse abundance peaks and other resource availability are low on the island in the fall months when the isotopic niches of house mice and salamanders overlap significantly indicating the potential for competition, most likely for arthropod prey.DiscussionOur results indicate how seasonal shifts in both mouse abundance and resource availability are key factors that mediate the consumptive and competitive impacts of introduced house mice on this island ecosystem. As mice consume and/or compete with a wide range of native taxa, eradication has the potential to provide wide-reaching restoration benefits on Southeast Farallon Island. Post-eradication monitoring focused on plant, terrestrial invertebrate, salamander, and seabird populations will be crucial to confirm these predictions. creator: Michael J. Polito creator: Bret Robinson creator: Pete Warzybok creator: Russell W. Bradley uri: https://doi.org/10.7717/peerj.13904 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Polito et al. title: Cultivation has selected for a wider niche and large range shifts in maize link: https://peerj.com/articles/14019 last-modified: 2022-09-22 description: BackgroundMaize (Zea mays L.) is a staple crop cultivated on a global scale. However, its ability to feed the rapidly growing human population may be impaired by climate change, especially if it has low climatic niche and range lability. One important question requiring clarification is therefore whether maize shows high niche and range lability.MethodsWe used the COUE scheme (a unified terminology representing niche centroid shift, overlap, unfilling and expansion) and species distribution models to study the niche and range changes between maize and its wild progenitors using occurrence records of maize, lowland teosinte (Zea mays ssp. parviglumis) and highland teosinte (Zea mays ssp. mexicana), respectively, as well as explore the mechanisms underlying the niche and range changes.ResultsIn contrast to maize in Mexico, maize did not conserve its niche inherited from lowland and highland teosinte at the global scale. The niche breadth of maize at the global scale was wider than that of its wild progenitors (ca. 5.21 and 3.53 times wider compared with lowland and highland teosinte, respectively). Compared with its wild progenitors, maize at global scale can survive in regions with colder, wetter climatic conditions, as well as with wider ranges of climatic variables (ca. 4.51 and 2.40 times wider compared with lowland and highland teosinte, respectively). The niche changes of maize were largely driven by human introduction and cultivation, which have exposed maize to climatic conditions different from those experienced by its wild progenitors. Small changes in niche breadth had large effects on the magnitude of range shifts; changes in niche breadth thus merit increased attention.DiscussionOur results demonstrate that maize shows wide climatic niche and range lability, and this substantially expanded its realized niche and potential range. Our findings also suggest that niche and range shifts probably triggered by natural and artificial selection in cultivation may enable maize to become a global staple crop to feed the growing population and adapting to changing climatic conditions. Future analyses are needed to determine the limits of the novel conditions that maize can tolerate, especially relative to projected climate change. creator: Rujing Yang creator: Runyao Cao creator: Xiang Gong creator: Jianmeng Feng uri: https://doi.org/10.7717/peerj.14019 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Yang et al. title: Genome-wide identification, characterization and expression analysis of HAK genes and decoding their role in responding to potassium deficiency and abiotic stress in Medicago truncatula link: https://peerj.com/articles/14034 last-modified: 2022-09-22 description: BackgroundThe HAK family is the largest potassium (K+) transporter family, vital in K+ uptake, plant growth, and both plant biotic and abiotic stress responses. Although HAK family members have been characterized and functionally investigated in many species, these genes are still not studied in detail in Medicago truncatula, a good model system for studying legume genetics.MethodsIn this study, we screened the M. truncatula HAK family members (MtHAKs). Furthermore, we also conducted the identification, phylogenetic analysis, and prediction of conserved motifs of MtHAKs. Moreover, we studied the expression levels of MtHAKs under K+ deficiency, drought, and salt stresses using quantitative real-time PCR (qRT-PCR).ResultsWe identified 20 MtHAK family members and classified them into three clusters based on phylogenetic relationships. Conserved motif analyses showed that all MtHAK proteins besides MtHAK10 contained the highly conserved K+ transport domain (GVVYGDLGTSPLY). qRT-PCR analysis showed that several MtHAK genes in roots were induced by abiotic stress. In particular, MtHAK15, MtHAK17, and MtHAK18 were strongly up-regulated in the M. truncatula roots under K+ deficiency, drought, and salt stress conditions, thereby implying that these genes are good candidates for high-affinity K+ uptake and therefore have essential roles in drought and salt tolerance.DiscussionsOur results not only provided the first genetic description and evolutionary relationships of the K+ transporter family in M. truncatula, but also the potential information responding to K+ deficiency and abiotic stresses, thereby laying the foundation for molecular breeding of stress-resistant legume crops in the future. creator: Yanxue Zhao creator: Lei Wang creator: Pengcheng Zhao creator: Zhongjie Liu creator: Siyi Guo creator: Yang Li creator: Hao Liu uri: https://doi.org/10.7717/peerj.14034 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Zhao et al.