title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=682 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Variability within a clonal population of Erwinia amylovora disclosed by phenotypic analysis link: https://peerj.com/articles/13695 last-modified: 2022-07-21 description: BackgroundFire blight is a destructive disease of pome trees, caused by Erwinia amylovora, leading to high losses of chain-of-values fruits. Major outbreaks were registered between 2010 and 2017 in Portugal, and the first molecular epidemiological characterization of those isolates disclosed a clonal population with different levels of virulence and susceptibility to antimicrobial peptides.MethodsThis work aimed to further disclose the genetic characterization and unveil the phenotypic diversity of this E. amylovora population, resorting to MLSA, growth kinetics, biochemical characterization, and antibiotic susceptibility.ResultsWhile MLSA further confirmed the genetic clonality of those isolates, several phenotypic differences were recorded regarding their growth, carbon sources preferences, and chemical susceptibility to several antibiotics, disclosing a heterogeneous population. Principal component analysis regarding the phenotypic traits allows to separate the strains Ea 630 and Ea 680 from the remaining.DiscussionRegardless the genetic clonality of these E. amylovora strains isolated from fire blight outbreaks, the phenotypic characterization evidenced a population diversity beyond the genotype clonality inferred by MLSA and CRISPR, suggesting that distinct sources or environmental adaptations of this pathogen may have occurred.ConclusionAttending the characteristic clonality of E. amylovora species, the data gathered here emphasizes the importance of phenotypic assessment of E. amylovora isolates to better understand their epidemiological behavior, namely by improving source tracking, make risk assessment analysis, and determine strain-specific environmental adaptations, that might ultimately lead to prevent new outbreaks. creator: Rafael J. Mendes creator: Conceição Amaro creator: João Pedro Luz creator: Fernando Tavares creator: Conceição Santos uri: https://doi.org/10.7717/peerj.13695 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Mendes et al. title: Identification and validation of immune related core transcription factors GTF2I in NAFLD link: https://peerj.com/articles/13735 last-modified: 2022-07-21 description: BackgroundNonalcoholic fatty liver disease (NAFLD) is the most common liver disease worldwide that endangers human health. Transcription factors (TFs) have gradually become hot spots for drug development in NAFLD for their impacts on metabolism. However, the specific TFs that regulate immune response in the development of NAFLD is not clear. This study aimed to investigate the TFs involved in the immune response of NAFLD and provide novel targets for drug development.MethodsMicroarray data were obtained from liver samples from 26 normal volunteers and 109 NAFLD patients using the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were analyzed by limma package. Differentially expressed transcription factors (DETFs) were obtained on DEGs combined with Cistrome Cancer database. Immune signatures and pathways hallmark were identified by ssGSSEA and GSVA. The co-regulation network was constructed by the above results. Further, quantitative Real-time Polymerase Chain Reaction (qRT-PCR), Western blot (WB) and Immunohistochemistry (IHC) were used to validate the relationship between GTF2I and NAFLD. CIBERSORT analysis was performed to identify cell types to explore the relationship between differential expression of GTF2I and immune cell surface markers.ResultsA total of 617 DEGs and six DETFs (ESR1, CHD2, GTF2I, EGR1, HCFC1, SP2) were obtained by differential analysis. Immune signatures and pathway hallmarks were identified by ssGSSEA and GSVA. GTF2I and CHD2 were screened through the co-regulatory networks of DEGs, DETFs, immune signatures and pathway hallmarks. Furthermore, qRT-PCR, WB and IHC indicated that GTF2I but not CHD2 was significantly upregulated in NAFLD. Finally, in silico, our data confirmed that GTF2I has a wide impact on the immune profile by negatively regulating the expression of the chemokine receptor family (227/261, count of significance).ConclusionGTF2I plays a role in NAFLD by negatively regulating the chemokine receptor family, which affects the immune profile. This study may provide a potential target for the diagnosis or therapy of NAFLD. creator: Minbo Zhang creator: Yu Zhang creator: Xiaoxiao Jiao creator: Linying Lai creator: Yiting Qian creator: Bo Sun creator: Wenzhuo Yang uri: https://doi.org/10.7717/peerj.13735 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: The function of small RNA in Pseudomonas aeruginosa link: https://peerj.com/articles/13738 last-modified: 2022-07-21 description: Pseudomonas aeruginosa, the main conditional pathogen causing nosocomial infection, is a gram-negative bacterium with the largest genome among the known bacteria. The main reasons why Pseudomonas aeruginosa is prone to drug-resistant strains in clinic are: the drug-resistant genes in its genome and the drug resistance easily induced by single antibiotic treatment. With the development of high-throughput sequencing technology and bioinformatics, the functions of various small RNAs (sRNA) in Pseudomonas aeruginosa are being revealed. Different sRNAs regulate gene expression by binding to protein or mRNA to play an important role in the complex regulatory network. In this article, first, the importance and biological functions of different sRNAs in Pseudomonas aeruginosa are explored, and then the evidence and possibilities that sRNAs served as drug therapeutic targets are discussed, which may introduce new directions to develop novel disease treatment strategies. creator: Pei Liu creator: Changwu Yue creator: Lihua Liu creator: Can Gao creator: Yuhong Lyu creator: Shanshan Deng creator: Hongying Tian creator: Xu Jia uri: https://doi.org/10.7717/peerj.13738 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Liu et al. title: Soil carbon sequestration potential in global croplands link: https://peerj.com/articles/13740 last-modified: 2022-07-21 description: Improving the amount of organic carbon in soils is an attractive alternative to partially mitigate climate change. However, the amount of carbon that can be potentially added to the soil is still being debated, and there is a lack of information on additional storage potential on global cropland. Soil organic carbon (SOC) sequestration potential is region-specific and conditioned by climate and management but most global estimates use fixed accumulation rates or time frames. In this study, we model SOC storage potential as a function of climate, land cover and soil. We used 83,416 SOC observations from global databases and developed a quantile regression neural network to quantify the SOC variation within soils with similar environmental characteristics. This allows us to identify similar areas that present higher SOC with the difference representing an additional storage potential. We estimated that the topsoils (0–30 cm) of global croplands (1,410 million hectares) hold 83 Pg C. The additional SOC storage potential in the topsoil of global croplands ranges from 29 to 65 Pg C. These values only equate to three to seven years of global emissions, potentially offsetting 35% of agriculture’s 85 Pg historical carbon debt estimate due to conversion from natural ecosystems. As SOC store is temperature-dependent, this potential is likely to reduce by 14% by 2040 due to climate change in a “business as usual” scenario. The results of this article can provide a guide to areas of focus for SOC sequestration, and highlight the environmental cost of agriculture. creator: José Padarian creator: Budiman Minasny creator: Alex McBratney creator: Pete Smith uri: https://doi.org/10.7717/peerj.13740 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Padarian et al. title: Growth parameters and responses of green algae across a gradient of phototrophic, mixotrophic and heterotrophic conditions link: https://peerj.com/articles/13776 last-modified: 2022-07-21 description: Many studies have shown that algal growth is enhanced by organic carbon and algal mixotrophy is relevant for physiology and commercial cultivation. Most studies have tested only a single organic carbon concentration and report different growth parameters which hampers comparisons and improvements to algal cultivation methodology. This study compared growth of green algae Chlorella vulgaris and Chlamydomonas reinhardtii across a gradient of photoautotrophic-mixotrophic-heterotrophic culture conditions, with five acetate concentrations. Culture growth rates and biomass achieved were compared using different methods of biomass estimation. Both species grew faster and produced the most biomass when supplied with moderate acetate concentrations (1–4 g L−1), but light was required to optimize growth rates, biomass yield, cell size and cell chlorophyll content. Higher acetate concentration (10 g L−1) inhibited algal production. The choice of growth parameter and method to estimate biomass (optical density (OD), chlorophyll a fluorescence, flow cytometry, cell counts) affected apparent responses to organic carbon, but use of OD at 600, 680 or 750 nm was consistent. There were apparent trade-offs among exponential growth rate, maximum biomass, and culture time spent in exponential phase. Different cell responses over 1–10 g L−1 acetate highlight profound physiological acclimation across a gradient of mixotrophy. In both species, cell size vs cell chlorophyll relationships were more constrained in photoautotrophic and heterotrophic cultures, but under mixotrophy, and outside exponential growth phase, these relationships were more variable. This study provides insights into algal physiological responses to mixotrophy but also has practical implications for choosing parameters for monitoring commercial algal cultivation. creator: Erica B. Young creator: Lindsay Reed creator: John A. Berges uri: https://doi.org/10.7717/peerj.13776 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Young et al. title: FastANI, Mash and Dashing equally differentiate between Klebsiella species link: https://peerj.com/articles/13784 last-modified: 2022-07-21 description: Bacteria of the genus Klebsiella are among the most important multi-drug resistant human pathogens, though they have been isolated from a variety of environments. The importance and ubiquity of these organisms call for quick and accurate methods for their classification. Average Nucleotide Identity (ANI) is becoming a standard for species delimitation based on whole genome sequence comparison. However, much faster genome comparison tools have been appearing in the literature. In this study we tested the quality of different approaches for genome-based species delineation against ANI. To this end, we compared 1,189 Klebsiella genomes using measures calculated with Mash, Dashing, and DNA compositional signatures, all of which run in a fraction of the time required to obtain ANI. Receiver Operating Characteristic (ROC) curve analyses showed equal quality in species discrimination for ANI, Mash and Dashing, with Area Under the Curve (AUC) values above 0.99, followed by DNA signatures (AUC: 0.96). Accordingly, groups obtained at optimized cutoffs largely agree with species designation, with ANI, Mash and Dashing producing 15 species-level groups. DNA signatures broke the dataset into more than 30 groups. Testing Mash to map species after adding draft genomes to the dataset also showed excellent results (AUC above 0.99), producing a total of 26 Klebsiella species-level groups. The ecological niches of Klebsiella strains were found to neither be related to species delimitation, nor to protein functional content, suggesting that a single Klebsiella species can have a wide repertoire of ecological functions. creator: Julie E. Hernández-Salmerón creator: Gabriel Moreno-Hagelsieb uri: https://doi.org/10.7717/peerj.13784 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Hernández-Salmerón and Moreno-Hagelsieb title: Cross-sectional associations between effort-reward imbalance at work and oral diseases in Japan link: https://peerj.com/articles/13792 last-modified: 2022-07-21 description: BackgroundPsychological stress is a potential risk factor for oral diseases. However, evidence for the association between work stress and oral diseases is scarce. We aimed to examine the associations of work stress, according to the effort-reward imbalance model, with dental caries, periodontal status, and tooth loss.MethodsThis cross-sectional study included 184 regular employees at a medical university and 435 registrants of a web research company. Work stress was assessed using the effort-reward imbalance (ERI) ratio. Dental caries and tooth loss were assessed according to the number of decayed, filled, and missing teeth (DMFT) among the set of 28 teeth. Periodontal status was assessed using a self-administered questionnaire. For the DMFT, a linear regression model was used to estimate the unstandardised coefficients. A Poisson regression model was used to estimate the prevalence ratios (PRs) of poor periodontal status.ResultsAmong medical university employees and employees enrolled from among the registrants of an online research company, a one-unit increase in the ERI ratio was associated with −2.81 (95% CI [−4.70 to −0.92]; p-value = 0.004) and −0.84 (95% CI [−1.80 to 0.12]; p-value = 0.085) changes in the DMFT from adjusted linear regression models, respectively. In employees enrolled from among the registrants of an online research company, a one-unit increase in the ERI ratio was also associated with 1.55 (95% CI [1.04–2.32]; p-value = 0.032) of the PR for poor periodontal status based on Poisson regression models.ConclusionERI at work was associated with an increased risk of poor periodontal status. creator: Yukihiro Sato creator: Eiji Yoshioka creator: Masanori Takekawa creator: Yasuaki Saijo uri: https://doi.org/10.7717/peerj.13792 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sato et al. title: Effects of growing Coptis chinensis Franch in the natural understory vs. under a manmade scaffold on its growth, alkaloid contents, and rhizosphere soil microenvironment link: https://peerj.com/articles/13676 last-modified: 2022-07-20 description: BackgroundThe main planting modes currently used for the production of Coptis chinensis Franch are under the shade of a manmade scaffold or a natural understory. In this study, we analysed changes in the growth, development, and alkaloids of C. chinensis when grown in a natural understory compared with under a manmade scaffold. We also clarified the differences in the rhizosphere soil microenvironment, represented by soil physicochemical factors, enzyme activity, and microbial community structure of 1- to 5-year-old C. chinensis between the different planting modes. These results will provide theoretical guidance and scientific evidence for the development, application, and extension of ecological planting technologies for C. chinensis.ResultsThe results of this study showed that rhizome length, rhizome diameter, and rhizome weight all increased over time in both planting modes. The greatest rhizome length was reached in 4-year-old C. chinensis, while the greatest rhizome diameter and rhizome weight were obtained in 5-year-old C. chinensis. There was no significant difference in rhizome biomass between the two planting modes. The alkaloid content of the four common alkaloids in the rhizome of 5-year-old C. chinensis at the harvest stage met the standards found in the Pharmacopoeia of the People’s Republic of China; the berberine content and total alkaloids in the rhizomes were significantly higher with natural understory planting compared to planting under a manmade scaffold. A redundancy analysis revealed that the physicochemical factors and enzyme activity of rhizosphere soil were significantly correlated with variation in microbial community structure. Soil pH, available potassium, bulk density, available nitrogen, catalase, and peroxidase were all significantly correlated with bacterial and fungal community structures. Among these, soil pH was the most important factor influencing the structures of the fungal and bacterial community. In the two planting modes, the differences in soil enzyme activity and microbial community structure mainly manifested in the rhizosphere soil of C. chinensis between different growth years, as there was little difference between the rhizosphere soil of C. chinensis in a given growth year under different planting modes. The levels of nitrogen, phosphorus, potassium, and organic matter in the rhizosphere soil under either planting mode were closely associated with the type and amount of fertiliser applied to C. chinensis. Investigating the influence of different fertilisation practices on nutrient cycling in farmland and the relationship between fertilisation and the soil environment will be key to improving the yield and quality of C. chinensis medicinal materials while maintaining the health of the soil microenvironment. creator: Yu Wang creator: Yu R. Mo creator: Jun Tan creator: Li X. Wu creator: Yuan Pan creator: Xia D. Chen uri: https://doi.org/10.7717/peerj.13676 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Evaluating the readability, quality and reliability of online patient education materials on post-covid pain link: https://peerj.com/articles/13686 last-modified: 2022-07-20 description: BackgroundThe use of the Internet to access healthcare-related information is increasing day by day. However, there are concerns regarding the reliability and comprehensibility of this information. This study aimed to investigate the readability, reliability, and quality of Internet-based patient educational materials (PEM) related to “post-COVID-19 pain.”MethodsOne-hundred websites that fit the purposes of the study were identified by searching for the terms “post-COVID-19 pain” and “pain after COVID-19” using the Google search engine on February 24, 2022. The website readability was assessed using the Flesch Reading Ease Score (FRES), Flesch–Kincaid Grade Level (FKGL), Simple Measure of Gobbledygook (SMOG), and Gunning FOG (GFOG). The reliability, quality, and popularity of the websites were assessed using the JAMA score, DISCERN score/Health on the Net Foundation code of conduct, and Alexa, respectively.ResultsUpon investigation of the textual contents, the mean FRES was 51.40 ± 10.65 (difficult), the mean FKGL and SMOG were 10.93 ± 2.17 and 9.83 ± 1.66 years, respectively, and the mean GFOG was 13.14 ± 2.16 (very difficult). Furthermore, 24.5% of the websites were highly reliable according to JAMA scores, 8% were of high quality according to GQS values, and 10% were HONcode-compliant. There was a statistically significant difference between the website types and reliability (p = 0.003) and quality scores (p = 0.002).ConclusionThe readability level of PEM on post-COVID-19 pain was considerably higher than grade 6 educational level, as recommended by the National Institutes of Health, and had low reliability and poor quality. We suggest that Internet-based PEM should have a certain degree of readability that is in accordance with the educational level of the general public and feature reliable content. creator: Erkan Ozduran creator: Sibel Büyükçoban uri: https://doi.org/10.7717/peerj.13686 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Ozduran and Büyükçoban title: Baleen whale inhalation variability revealed using animal-borne video tags link: https://peerj.com/articles/13724 last-modified: 2022-07-20 description: Empirical metabolic rate and oxygen consumption estimates for free-ranging whales have been limited to counting respiratory events at the surface. Because these observations were limited and generally viewed from afar, variability in respiratory properties was unknown and oxygen consumption estimates assumed constant breath-to-breath tidal volume and oxygen uptake. However, evidence suggests that cetaceans in human care vary tidal volume and breathing frequency to meet aerobic demand, which would significantly impact energetic estimates if the findings held in free-ranging species. In this study, we used suction cup-attached video tags positioned posterior to the nares of two humpback whales (Megaptera novaeangliae) and four Antarctic minke whales (Balaenoptera bonaerensis) to measure inhalation duration, relative nares expansion, and maximum nares expansion. Inhalation duration and nares expansion varied between and within initial, middle, and terminal breaths of surface sequences between dives. The initial and middle breaths exhibited the least variability and had the shortest durations and smallest nares expansions. In contrast, terminal breaths were highly variable, with the longest inhalation durations and the largest nares expansions. Our results demonstrate breath-to-breath variability in duration and nares expansion, suggesting differential oxygen exchange in each breath during the surface interval. With future validation, inhalation duration or nares area could be used alongside respiratory frequency to improve oxygen consumption estimates by accounting for breath-to-breath variation in wild whales. creator: Emily C. Nazario creator: David E. Cade creator: K.C. Bierlich creator: Max F. Czapanskiy creator: Jeremy A. Goldbogen creator: Shirel R. Kahane-Rapport creator: Julie M. van der Hoop creator: Merceline T. San Luis creator: Ari S. Friedlaender uri: https://doi.org/10.7717/peerj.13724 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nazario et al.