title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=594 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genetic diversity of Venturia inaequalis isolates from the scabs in apple trees in Gansu Province, China, using AFLP markers link: https://peerj.com/articles/14512 last-modified: 2022-12-16 description: Apple scab is a serious disease that restricts the growth of cultivated apples. The objective of this study is to investigate the genetic variations and genetic structure of Venturia inaequalis in Gansu Province, China. 108 isolates of the pathogen V. inaequalis from the Jingning, Lingtai, Jingchuan, Xifeng, Ning and Maiji regions were collected, and their genetic diversity was analyzed using AFLP molecular marker technique. The results showed that genetic diversity was present among the isolates but was not statistically significant. Genetic distance values ranged from 0.0095 to 0.0762. Cluster analysis results showed that the 108 isolates could be divided into two clusters using a similarity coefficient of 0.69. A total of 104 isolates were contained in cluster I while four isolates were contained in Cluster II. From the AMOVA analysis, 98% of variations were observed within the same region, while 2% were observed across different regions. The analysis of population structure showed that 108 isolates had two common ancestors, with the Jingning isolates mainly being derived from the red ancestor. PCoA analysis showed that the Jingning isolates were independent to a certain extent. The different geographical location caused the genetic difference of the isolates. The genetic diversity of apple scab in Gansu Province is greatly aided by this work, which also offers a theoretical foundation for the use of molecular markers in assisted breeding to create novel resistant types. creator: Zhaolong Lü creator: Nana Hui creator: Li Wang creator: Guo Zheng creator: Senshan Wang creator: Jiping Li uri: https://doi.org/10.7717/peerj.14512 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Lü et al. title: Metal tolerance capacity and antioxidant responses of new Salix spp. clones in a combined Cd-Pb polluted system link: https://peerj.com/articles/14521 last-modified: 2022-12-16 description: To investigate the physiochemical characteristics of two new clones, Salix matsudana ‘J172’ (A7) and Salix matsudana ‘Yankang1’ (A64) in combined Cd-Pb contaminated systems, a hydroponic experiment was designed. The plant biomass, photosynthesis, antioxidant responses and the accumulation of metals in different plant parts (leaf, stem, and root) were measured after 35-day treatments with Cd (15, 30 µM) and Pb (250, 500 µM). The results showed that exposure to Cd-Pb decreased the biomass but increased the net photosynthetic rate for both A7 and A64, demonstrating that photosynthesis may be one of the metabolic processes used to resist Cd-Pb stress. Compared with control, roots exposed to Cd-Pb had higher activity of superoxide dismutase and more malondialdehyde concentrations, which indicated the roots of both clones were apt to be damaged. The concentrations of soluble protein were obviously higher in the roots of A64 than A7, indicating the roles of the antioxidative substance were different between two willow clones. Soluble protein also had significant relationship with translocation factors from accumulation in roots of A64, which illustrated it played important roles in the tolerance of A64 roots to heavy metals. The roots could accumulate more Pb rather than transport to the shoots compared with Cd. The tolerance index was more than 85% on average for both clones under all the treatments, indicating their tolerance capacities to the combined stress of Cd and Pb are strong under the tested metal levels. Both clones are the good candidates for phytoremediation of Cd and Pb by the root filtration in the combined contamination environment. creator: Chuanfeng Zhang creator: Baoshan Yang creator: Hui Wang creator: Xiaohan Xu creator: Jiaxing Shi creator: Guanghua Qin uri: https://doi.org/10.7717/peerj.14521 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al. title: Effect of hyperglycemia on the immune function of COVID-19 patients with type 2 diabetes mellitus: a retrospective study link: https://peerj.com/articles/14570 last-modified: 2022-12-16 description: PurposeTo analyze the clinical characteristics and immune function parameters and to explore the effect of hyperglycemia on the immune function in patients with Corona Virus Disease 2019 (COVID-19) with type 2 diabetes mellitus (T2DM).MethodsThis retrospective study included patients with COVID-19 with T2DM hospitalized in Renmin Hospital of Wuhan University between January 31, 2020, and February 10, 2020. The clinical data were collected and patients were divided into a well-controlled group (blood glucose 3.9–10.0 mmol/L) and a poorly-controlled group (blood glucose >10.0 mmol/L). The differences in routine blood tests, peripheral lymphocyte subsets, humoral immune components, C-reactive protein (CRP) level, and cytokines were compared, and the correlation between blood glucose and immune parameters as well as the severity of the disease was analyzed.ResultsA total of 65 patients with COVID-19 and T2DM were included in the final analysis. Compared with the well-controlled group, patients in the poorly-controlled group had decreased lymphocytes, CD16+ 56+ NK cells, CD3+ T cells, CD8+ T cells and increased neutrophil percentage, IL-6 levels, CRP levels and serum concentration of IgA. Blood glucose was inversely correlated with CD16+ 56+ NK cells, CD3+ T cells, CD4+ T cells, and CD8+ T cells and positively correlated with IL-6 and CRP levels. There was a positive correlation between blood glucose and the severity of the COVID-19.ConclusionHyperglycemia will aggravate the immune dysfunction of COVID-19 patients with T2DM and affect the severity of COVID-19. creator: Ye Wang creator: Bo Yi creator: Shujun Wang creator: Xiaolin Chen creator: Zhongyuan Wen uri: https://doi.org/10.7717/peerj.14570 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al. title: Mitochondria and chloroplasts function in microalgae energy production link: https://peerj.com/articles/14576 last-modified: 2022-12-16 description: Microalgae are organisms that have the ability to perform photosynthesis, capturing CO2 from the atmosphere to produce different metabolites such as vitamins, sugars, lipids, among others, many of them with different biotechnological applications. Recently, these microorganisms have been widely studied due to their possible use to obtain clean energy. It has been postulated that the growth of microalgae and the production of high-energy metabolites depend on the correct function of cellular organelles such as mitochondria and chloroplasts. Thus, the development of different genetic tools to improve the function of these organelles is of high scientific and technological interest. In this paper we review the recent advances in microalgae engineering and the role of cellular organelles in order to increase cell productivity and biomass. creator: Diego F. Gomez-Casati creator: Julieta Barchiesi creator: Maria V. Busi uri: https://doi.org/10.7717/peerj.14576 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Gomez-Casati et al. title: Functional groups of Afrotropical EPT (Ephemeroptera, Plecoptera and Trichoptera) as bioindicators of semi-urban pollution in the Tsitsa River Catchment, Eastern Cape, South Africa link: https://peerj.com/articles/13970 last-modified: 2022-12-15 description: We examined the distribution patterns of Ephemeroptera, Plecoptera, and Trichoptera functional feeding groups (EPT FFGs) in five streams that drain semi-urban landscapes in the Tsitsa River catchment, Eastern Cape Province of South Africa. We undertook macroinvertebrate and physicochemical analysis over four seasons between 2016 and 2017 at eight sites in three land-use categories (Sites 1, 2 and 3), representing an increasing gradient of semi-urban pollution. Five EPT FFGs (shredders, grazers/scrapers, predators, collector-gatherers and collector-filterers) were fuzzy coded and analyzed using RLQ-R (environmental characteristics of samples), L (taxa distribution across samples) and Q (species traits) and fourth-corner analyses. Physicochemical variables, including phosphate-phosphorus, total inorganic nitrogen and temperature, were the most influential variables that significantly influenced the distribution patterns of EPT FFGs in the Tsitsa River. RLQ and the fourth-corner model revealed varying responses of FFGs to semi-urban pollution. Of the five FFGs, collectors were the most abundant EPT FFGs in the study area, exhibiting disparate responses to disturbances, with collector-gatherers associated with impacted sites and significantly associated with phosphate-phosphorus. On the other hand, collector-filterers decreased with increasing semi-urban disturbance and exhibited a significant negative association with phosphate-phosphorus, total inorganic nitrogen and temperature. Overall, this study provides further insights into the environmental factors that influence the distribution patterns of FFGs in Afrotropical streams and the potential use of FFGs as indicators of anthropogenic pollution in tropical streams and rivers. creator: Frank Chukwuzuoke Akamagwuna creator: Augustine Ovie Edegbene creator: Phindiwe Ntloko creator: Francis Ofurum Arimoro creator: Chika Felicitas Nnadozie creator: Dennis Junior Choruma creator: Oghenekaro Nelson Odume uri: https://doi.org/10.7717/peerj.13970 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Akamagwuna et al. title: Impacts of river fragmentation on limiting individual dietary specialization of Amazonian predatory fish link: https://peerj.com/articles/14266 last-modified: 2022-12-15 description: Individual dietary specialization is one of the factors that promotes variation in resource use at the individual level. Here we used stable isotope analysis of multiple tissues with different turnover rates to examine the degree of individual specialization in two sub-populations of the predator Cichla temensis inhabiting both fragmented and undammed rivers within the Uatumã River basin of the Amazon. Our results showed that the undammed river provides better conditions to promote individual dietary specialization than the fragmented river. This study contributes to the understanding of how specific life history characteristics of populations of generalist predators are impacted by fragmentation within megadiverse environments such as the Amazon basin. creator: Jamerson Aguiar-Santos creator: Pieter deHart creator: Bruce Forsberg creator: Carlos Freitas uri: https://doi.org/10.7717/peerj.14266 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Aguiar-Santos et al. title: Neospongodes atlantica, a potential case of an early biological introduction in the Southwestern Atlantic link: https://peerj.com/articles/14347 last-modified: 2022-12-15 description: Soft corals (Anthozoa: Octocorallia) are discreet components in the Southwestern Atlantic reef communities. In Brazil, the native octocoral shallow-reef fauna is mostly represented by gorgonians. Consequently, except for the nephtheid Neospongodes atlantica, most of the known soft corals from this region are considered non-indigenous. Hitherto, the monotypic genus Neospongodes, which was proposed in the early 1900s, has been considered to be endemic to the Northeastern Brazilian coast. Herein, based on in situ records, we show that N. atlantica is a substrate generalist that has been probably expanding its distribution by dominating extensive shallow and mesophotic sandy and reef bottoms, generally outcompeting other reef benthic organisms, including Brazilian endemic species. Based on previously unidentified museum specimens, new records, and a broad literature review, we provide the most comprehensive modelling of the potential distribution of this species in the Southwestern Atlantic. Based on molecular inference supported by in-depth morphological analysis, the probable non-indigenous and, therefore, ancient introduction of N. atlantica in Brazilian waters is discussed. Finally, these results support that Neospongodes and the Indo-Pacific Stereonephthya are synonyms, which led us to propose the latter as taxonomically invalid. creator: Ralf T.S. Cordeiro creator: Ágatha Nascimento Carpinelli creator: Ronaldo B. Francini-Filho creator: Barbara de Moura Neves creator: Carlos D. Pérez creator: Umberto de Oliveira creator: Paulo Sumida creator: Henrique Maranhão creator: Leonardo H.U. Monteiro creator: Pedro Carneiro creator: Marcelo V. Kitahara uri: https://doi.org/10.7717/peerj.14347 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Cordeiro et al. title: Using a real-world network to model the trade-off between stay-at-home restriction, vaccination, social distancing and working hours on COVID-19 dynamics link: https://peerj.com/articles/14353 last-modified: 2022-12-15 description: BackgroundHuman behaviour, economic activity, vaccination, and social distancing are inseparably entangled in epidemic management. This study aims to investigate the effects of various parameters such as stay-at-home restrictions, work hours, vaccination, and social distance on the containment of pandemics such as COVID-19.MethodsTo achieve this, we have developed an agent based model based on a time-dynamic graph with stochastic transmission events. The graph is constructed from a real-world social network. The edges of graph have been categorized into three categories: home, workplaces, and social environment. The conditions needed to mitigate the spread of wild-type COVID-19 and the delta variant have been analyzed. Our purposeful agent based model has carefully executed tens of thousands of individual-based simulations. We propose simple relationships for the trade-offs between effective reproduction number (Re), transmission rate, working hours, vaccination, and stay-at-home restrictions.ResultsWe have found that the effect of a 13.6% increase in vaccination for wild-type (WT) COVID-19 is equivalent to reducing four hours of work or a one-day stay-at-home restriction. For the delta, 20.2% vaccination has the same effect. Also, since we can keep track of household and non-household infections, we observed that the change in household transmission rate does not significantly alter the Re. Household infections are not limited by transmission rate due to the high frequency of connections. For the specifications of COVID-19, the Re depends on the non-household transmissions rate.ConclusionsOur findings highlight that decreasing working hours is the least effective among the non-pharmaceutical interventions. Our results suggest that policymakers decrease work-related activities as a last resort and should probably not do so when the effects are minimal, as shown. Furthermore, the enforcement of stay-at-home restrictions is moderately effective and can be used in conjunction with other measures if absolutely necessary. creator: Ramin Nashebi creator: Murat Sari creator: Seyfullah Kotil uri: https://doi.org/10.7717/peerj.14353 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Nashebi et al. title: Prevalence of text neck posture, smartphone addiction, and its association with neck disorders among university students in the Kingdom of Saudi Arabia during the COVID-19 pandemic link: https://peerj.com/articles/14443 last-modified: 2022-12-15 description: The smartphone emerges as an inevitable gadget in modern society and its increased usage results in neck disorders among its users. However, the factors associated with neck disorders among smartphone users are ambiguous and less explored in the literature. The purpose of this research was to determine the prevalence of text neck posture, smartphone addiction/overuse, and its association with neck disorders among university students in the Kingdom of Saudi Arabia during the COVID-19 pandemic. A total of 313 university students who were aged 18 years and older, owned a smartphone, and used it during the preceding 12 months participated in this cross-sectional study. A self-administered questionnaire was used to collect data regarding the prevalence of text neck posture, smartphone addiction/overuse, neck disorders, and the level of physical activity. Binary logistic regression was used to determine the association between the prevalence of neck disorders and text neck posture, smartphone addiction/overuse, and level of physical activity. The 12 months prevalence of neck disorders due to smartphone use among the participants was found to be 46%. The neck disorders were more prevalent among participants who reported text neck posture (P < 0.001) and categorized as smartphone-addicted/overuse (P < 0.001). Measures to promote the awareness of healthy use of smartphones including postural education and to decrease its screen time are warranted to reduce neck disorders. creator: Mohamed Sherif Sirajudeen creator: Msaad Alzhrani creator: Ahmad Alanazi creator: Mazen Alqahtani creator: Mohamed Waly creator: Radhakrishnan Unnikrishnan creator: Hariraja Muthusamy creator: Wafa Alrubaia creator: Nidaa Alanazi creator: Mohamed K. Seyam creator: Faizan Kashoo creator: Mohammad Miraj creator: Shashikumar Channmgere Govindappa creator: Khalid Ahmed Alghamdi creator: Nasser M. Al-Hussinan uri: https://doi.org/10.7717/peerj.14443 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Sirajudeen et al. title: Association between the CASC16 rs4784227 polymorphism and breast cancer risk and prognosis in a northeast Chinese Han population link: https://peerj.com/articles/14462 last-modified: 2022-12-15 description: BackgroundBreast cancer (BC) poses a serious threat to women worldwide. This research was designed to explore the association between the rs4784227 polymorphism of cancer susceptibility candidate gene 16 (CASC16) and BC susceptibility and prognosis, aiming to provide further information for the early detection of BC and to accelerate comprehensive cancer management.MethodsA total of 1,733 subjects were recruited for this case-control study, of which 828 are BC patients and 905 are healthy individuals. The relevance between SNP rs4784227 and BC risk in diverse genetic models was analyzed by using the SNPStats analysis program and was assessed by odds ratios (ORs) and 95% confidence intervals (CIs) using the binary logistic regression model. Pearson’s χ2 test was used to determine the correlation between the polymorphism and clinical characteristics of BC patients. Additionally, univariate survival analysis was performed by the Kaplan-Meier method and log-rank test, and multivariate survival analysis was performed by Cox regression.ResultsSNP rs4784227 was significantly associated with susceptibility to BC in the dominant model (CT/TT versus CC, OR = 1.237, 95% CI = 1.012–1.513, P = 0.038). The minor allele of SNP rs4784227 was significantly linked to an increased risk of BC (OR = 1.197, 95% CI = 1.022–1.401, P = 0.026). In addition, the rs4784227 polymorphism of CASC16 was associated with perineural invasion (P = 0.030), menstrual status (P = 0.016) and histological grade (P = 0.001, P = 0.003, P = 0.025; respectively) of BC patients. There was no significant association between the genotypes of rs4784227 and disease-free survival (DFS) or overall survival (OS) of breast cancer patients (P > 0.05).ConclusionsThe rs4784227 polymorphism of CASC16 may affect susceptibility to breast cancer and is associated with perineural invasion, menstrual status and histological grade in BC patients. Additionally, our results could not confirm that this polymorphism was related to breast cancer prognosis. creator: Yue Zhang creator: Changgui Kou creator: Lin Jia creator: Yangyang Gao creator: Xin Li creator: Hao Wu creator: Naifei Chen creator: Zheng Lv uri: https://doi.org/10.7717/peerj.14462 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Zhang et al.