title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=479 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Urban biogeography of fungal endophytes across San Francisco link: https://peerj.com/articles/15454 last-modified: 2023-07-31 description: In natural and agricultural systems, the plant microbiome–the microbial organisms associated with plant tissues and rhizosphere soils–has been shown to have important effects on host physiology and ecology, yet we know little about how these plant-microbe relationships play out in urban environments. Here we characterize the composition of fungal communities associated with living leaves of one of the most common sidewalk trees in the city of San Francisco, California. We focus our efforts on endophytic fungi (asymptomatic microfungi that live inside healthy leaves), which have been shown in other systems to have large ecological effects on the health of their plant hosts. Specifically, we characterized the foliar fungal microbiome of Metrosideros excelsa (Myrtaceae) trees growing in a variety of urban environmental conditions. We used high-throughput culturing, PCR, and Sanger sequencing of the internal transcribed spacer nuclear ribosomal DNA (ITS nrDNA) region to quantify the composition and structure of fungal communities growing within healthy leaves of 30 M. excelsa trees from six distinct sites, which were selected to capture the range of environmental conditions found within city limits. Sequencing resulted in 854 high-quality ITS sequences. These sequences clustered into 85 Operational Taxonomic Units (97% OTUs). We found that these communities encompass relatively high alpha (within) and beta (between-site) diversity. Because the communities are all from the same host tree species, and located in relatively close geographical proximity to one another, these analyses suggest that urban environmental factors such as heat islands or differences in vegetation or traffic density (and associated air quality) may potentially be influencing the composition of these fungal communities. These biogeographic patterns provide evidence that plant microbiomes in urban environments can be as dynamic and complex as their natural counterparts. As human populations continue to transition out of rural areas and into cities, understanding the factors that shape environmental microbial communities in urban ecosystems stands to become increasingly important. creator: Emma Gibson creator: Naupaka B. Zimmerman uri: https://doi.org/10.7717/peerj.15454 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gibson and Zimmerman title: Dynamic assessment of the effectiveness of digital game-based literacy training in beginning readers: a cluster randomised controlled trial link: https://peerj.com/articles/15499 last-modified: 2023-07-31 description: In this article, we report on a study evaluating the effectiveness of a digital game-based learning (DGBL) tool for beginning readers of Dutch, employing active (math game) and passive (no game) control conditions. This classroom-level randomized controlled trial included 247 first graders from 16 classrooms in the Netherlands and the Dutch-speaking part of Belgium. The intervention consisted of 10 to 15 min of daily playing during school time for a period of up to 7 weeks. Our outcome measures included reading fluency, phonological skills, as well as purpose built in-game proficiency levels to measure written lexical decision and letter speech sound association. After an average of 28 playing sessions, the literacy game improved letter knowledge at a scale generalizable for all children in the classroom compared to the two control conditions. In addition to a small classroom wide benefit in terms of reading fluency, we furthermore discovered that children who scored high on phonological awareness prior to training were more fluent readers after extensive exposure to the reading game. This study is among the first to exploit game generated data for the evaluation of DGBL for literacy interventions. creator: Toivo Glatz creator: Wim Tops creator: Elisabeth Borleffs creator: Ulla Richardson creator: Natasha Maurits creator: Annemie Desoete creator: Ben Maassen uri: https://doi.org/10.7717/peerj.15499 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Glatz et al. title: Role of ELK1 in regulating colorectal cancer progression: miR-31-5p/CDIP1 axis in CRC pathogenesis link: https://peerj.com/articles/15602 last-modified: 2023-07-31 description: Background and ObjectiveColorectal cancer (CRC) is a malignant tumor that affects the digestive system. With the increased of modernization of society, the incidence of colorectal cancer has increased throughout the world. As a transcription factor, ELK1 has been widely studied in colorectal cancer. However, there are still many unknown factors regarding its specific mechanism of action.This study explored the role of ELK1 and its downstream pathway in CRC pathogenesis.MethodsBased on clinical samples, this study examined miR-31-5p expression in CRC cells and its impact on malignant behaviors (migration, invasion, apoptosis) and autophagy. The promoter sequence of miR-31-5p was obtained from the UCSC database, and ELK1 was identified as its transcription factor. In ELK1-knockdown CRC cells, miR-31-5p was overexpressed, and its response in malignant behaviors and autophagy was analyzed. The target gene CDIP1 was predicted and verified using a dual-luciferase assay. The influence of CDIP1 on malignant behavior in CRC cells was assessed, and CDIP1 siRNA was used as a rescue treatment for miR-31-5p inhibition. The role of ELK1/miR-31-5p in tumor growth was validated in vivo.ResultsmiR-31-5p expression was upregulated in the colorectal cancer tissues and cells. The knockdown of miR-31-5p markedly inhibited cancer cells’ malignant behaviors and mediated autophagy. ELK1 was confirmed to bind with the miR-31-5p promoter and enhance miR-31-5p transcription. miR-31-5p was found to bind with the CDIP1 3’UTR and inhibit CDIP1 expression. CDIP1 siRNA partially rescued the effects of miR-31-5p knockdown on cell metastatic ability, autophagy, and apoptosis. Based on the in vivo experiments, results showed that the ELK1/miR-31-5p axis positively regulated tumor growth in nude mice.ConclusionOur findings indicate that ELK1 regulates the progression of colorectal cancer via an miR-31-5p/CDIP1 axis, and the ELK1/miR-31-5p/CDIP1 axis could be a therapeutic target for colorectal cancer. creator: Guoqiang Yan creator: Lei Wang uri: https://doi.org/10.7717/peerj.15602 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yan and Lei title: International fitness scale (IFIS): association with motor performance in children with obesity link: https://peerj.com/articles/15765 last-modified: 2023-07-31 description: BackgroundOverweight and obesity are defined as abnormal or excessive fat accumulation that presents a risk to health; and compared with their normal-weight peers, these individuals tend to have a lower level of self-confidence, and consequently lower physical activity adherence. Due to these self-perceived barriers, the aim of our study was to evaluate the efficacy of an online training program on self-reported physical fitness (SRPF) in children with obesity (OB).MethodsA total of 32 children with OB carried out physical fitness (PF) tests and were asked to complete the International Fitness Enjoyment Scale (IFIS) questionnaire. The physical fitness tests were the Standing Broad Jump (SBJ), the 6-Min Walking Test (6MWT) and the 4 × 10 m sprint test. Children participated in a 3-weekly 60-min training session through Zoom platform. Before the beginning of the training protocol, OB children were compared with normal weight (NW) ones for PF batteries and the IFIS questionnaire. Changes in performances after the training were assessed by paired Student t and Wilcoxon tests.ResultsAfter the online training program children increased their performance in 6MWT (mean difference (MD) = 54.93; p < 0.0001) in SBJ (MD = 10.00; p = 0.0001) and in 4 × 10 m sprint test (MD = −0.78; p < 0.0001). No differences were found in children’s physical fitness perception.DiscussionOur study highlighted how a structured online training program can lead to improvements in PF of children with OB. Instead, the lack of differences in SRPF after the training suggests interesting questions to be explored on the aspects linked to self-perception. Therefore, even if our training protocol could not directly improve SRPF in children with obesity, the enhancement of their PF could be a starting point for achieving this result with a longer training period and consequently improve PA participation for children with OB. creator: Mariangela Valentina Puci creator: Caterina Cavallo creator: Alessandro Gatti creator: Vittoria Carnevale Pellino creator: Daniela Lucini creator: Valeria Calcaterra creator: Gianvincenzo Zuccotti creator: Nicola Lovecchio creator: Matteo Vandoni uri: https://doi.org/10.7717/peerj.15765 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Puci et al. title: Salt and osmotic stress can improve the editing efficiency of CRISPR/Cas9-mediated genome editing system in potato link: https://peerj.com/articles/15771 last-modified: 2023-07-31 description: CRISPR/Cas9-mediated genome editing technology has been widely used for the study of gene function in crops, but the differences between species have led to widely varying genome editing efficiencies. The present study utilized a potato hairy root genetic transformation system and incorporated a rapid assay with GFP as a screening marker. The results clearly demonstrated that salt and osmotic stress induced by NaCl (10 to 50 mM) and mannitol (50 to 200 mM) treatments significantly increased the positive rates of genetic transformation mediated by A. rhizogenes and the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato. However, it was observed that the regeneration of potato roots was partially inhibited as a result. The analysis of CRISPR/Cas9-mediated mutation types revealed that chimeras accounted for the largest proportion, ranging from 62.50% to 100%. Moreover, the application of salt and osmotic stress resulted in an increased probability of null mutations in potato. Notably, the highest rate of null mutations, reaching 37.5%, was observed at a NaCl concentration of 10 mM. Three potential off-target sites were sequenced and no off-targeting was found. In conclusion, the application of appropriate salt and osmotic stress significantly improved the editing efficiency of the CRISPR/Cas9-mediated genome editing system in potato, with no observed off-target effects. However, there was a trade-off as the regeneration of potato roots was partially inhibited. Overall, these findings present a new and convenient approach to enhance the genome editing efficiency of the CRISPR/Cas9-mediated gene editing system in potato. creator: Mingwang Ye creator: Mengfan Yao creator: Canhui Li creator: Ming Gong uri: https://doi.org/10.7717/peerj.15771 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ye et al. title: Expression and correlation of COX-2 and NUCB1 in colorectal adenocarcinoma link: https://peerj.com/articles/15774 last-modified: 2023-07-31 description: ObjectiveTo investigate the expression and correlation of COX-2 and NUCB1 in colorectal adenocarcinoma and adjacent tissues.MethodsThe expression of COX-2 and NUCB1 and their effects on prognosis were predicted using bioinformatics. Immunohistochemistry was used to identify the expression of two molecules in 56 cases of colorectal adenocarcinoma and the surrounding tissues. The expression of two molecules and their association with clinicopathological variables were examined using the chi-square test. The association between COX-2 and NUCB1 was investigated using the Spearman correlation test.ResultsThe STRING database revealed that COX-2 and NUCB1 were strongly linked. According to the UALCAN and HPA database, COX-2 was upregulated while NUCB1 was downregulated in colorectal adenocarcinoma, both at the protein and gene levels. The OS times for COX-2 and NUCB1 high expression, however, exhibited the same patterns. The rate of positive COX-2 immunohistochemical staining in cancer tissues was 69.64% (39/56), which was significantly higher than the rate in healthy tissues 28.57% (16/56). NUCB1 was expressed positively in cancer tissues at a rate of 64.29% (36/56) compared to just 19.64% (11/56) in neighboring tissues. The positive expression levels of COX-2 and NUCB1 were both closely related to clinical stage, differentiation degree, and lymphatic metastases (P < 0.05). In colorectal cancer, COX-2 and NUCB1 expression were significantly correlated (rs = 0.6312, P < 0.001).ConclusionBoth COX-2 and NUCB1 are overexpressed and significantly associated in colorectal adenocarcinoma. creator: Yuanyuan Zhang creator: Gai Zhang creator: Jinghua Zhong creator: An Li creator: Yanyang Wu creator: Zhenli Guo uri: https://doi.org/10.7717/peerj.15774 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zhang et al. title: The tetrapod fauna of the upper Permian Naobaogou Formation of China: 10. Jimusaria monanensis sp. nov. (Dicynodontia) shows a unique epipterygoid link: https://peerj.com/articles/15783 last-modified: 2023-07-31 description: Jimusaria is the first reported Chinese dicynodont, previously only known from Xinjiang. Here we refer two specimens from the Naobaogou Formation, Nei Mongol, China to Jimusaria based on the following features: squamosal separated from supraoccipital by tabular, tabular contacting opisthotic, sharp and thin lateral dentary shelf expanding anteriorly into a thick swelling, nasals fused as single element, rod-like medial bar formed by footplate of epipterygoid connecting to the parabasisphenoid and periotic medially. A new species, J. monanensis, is named based on the diagnostic characters on these two specimens such as distinct caniniform buttress lacking posteroventral furrow, naso-frontal suture forming an anterior directed sharp angle, and converging ventral ridges on posterior portion of anterior pterygoid rami. In Jimusaria, the epipterygoid posteromedially contacts the parabasisphenoid and the periotic as a rod-like bar, a unique morphology unknown in any other dicynodonts. This structure probably increases the stability of the palatal complex. A similar structure might also appear in other dicynodonts as a cartilage connection. The new occurrence of Jimusaria increases the diversity of the tetrapod assemblage from the Naobaogou Formation, and further strengthens the connection between the tetrapod faunas from Nei Mongol and Xinjiang. Based on the current record, Jimusaria is one of the few tetrapod genera which survived in the end-Permian mass extinction. creator: Yu-Tai Shi creator: Jun Liu uri: https://doi.org/10.7717/peerj.15783 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Shi and Liu title: The weathering process of carbonatite: weathering time link: https://peerj.com/articles/15793 last-modified: 2023-07-31 description: Soil formation by rock weathering is driven by a combination of parent material, climate, organisms, topography, and time. Among these soil-forming factors, time plays a pivotal role in the weathering of carbonatite but it is a challenging factor to study quantitatively. A method for determining the weathering duration of carbonatite based on its weathering characteristics over a century-scale time period has not been clearly established. In this study, we selected abandoned carbonatite tombstones commonly found in the karst region of southwest China for investigation, using the date when the tombstones were erected as the onset of weathering. Chemical weathering indices were used to evaluate the weathering degree of different oxide contents produced by the carbonatite weathering process. In order to explore the weathering characteristics over time, the relationship between weathering duration and weathering degree was established. The results showed the following: (1) magnesium (Mg), aluminum (Al), silicon (Si), iron (Fe), titanium (Ti) are gradually enriched in the carbonatite regolith, and calcium (Ca) is gradually reduced. (2) The chemical indices of alteration (CIA), leaching coefficient (Lc), alumina-to-calcium ratio (AC) and mobiles index (Imob) can be successfully used for evaluation of the weathering degree of the carbonatite in different weathering time periods. (3) During the weathering of carbonatite, the weathering rate is a logarithmic function of time. Our research shows that over a period of more than 100 years of weathering, the carbonatite weathering process is characterized by fast weathering rates and low weathering degree in the early stages, but slow weathering rates in the later stages. creator: Jin Chen creator: Fangbing Li creator: Xiangwei Zhao creator: Yang Wang creator: Limin Zhang creator: Ling Feng creator: Xiong Liu creator: Lingbin Yan creator: Lifei Yu uri: https://doi.org/10.7717/peerj.15793 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Green synthesis of silver nanoparticles using Ocimum sanctum Linn. and its antibacterial activity against multidrug resistant Acinetobacter baumannii link: https://peerj.com/articles/15590 last-modified: 2023-07-28 description: The biosynthesis of nanoparticles using the green route is an effective strategy in nanotechnology that provides a cost-effective and environmentally friendly alternative to physical and chemical methods. This study aims to prepare an aqueous extract of Ocimum sanctum (O. sanctum)-based silver nanoparticles (AgNPs) through the green route and test their antibacterial activity. The biosynthesized silver nanoparticles were characterised by colour change, UV spectrometric analysis, FTIR, and particle shape and size morphology by SEM and TEM images. The nanoparticles are almost spherical to oval or rod-shaped with smooth surfaces and have a mean particle size in the range of 55 nm with a zeta potential of −2.7 mV. The antibacterial activities of AgNPs evaluated against clinically isolated multidrug-resistant Acinetobacter baumannii (A. baumannii) showed that the AgNPs from O. sanctum are effective in inhibiting A. baumannii growth with a zone of inhibition of 15 mm in the agar well diffusion method and MIC and MBC of 32 µg/mL and 64 µg/mL, respectively. The SEM images of A. baumannii treated with AgNPs revealed damage and rupture in bacterial cells. The time-killing assay by spectrophotometry revealed the time- and dose-dependent killing action of AgNPs against A. baumannii, and the assay at various concentrations and time intervals indicated a statistically significant result in comparison with the positive control colistin at 2 µg/mL (P < 0.05). The cytotoxicity test using the MTT assay protocol showed that prepared nanoparticles of O. sanctum are less toxic against human cell A549. This study opens up a ray of hope to explore the further research in this area and to improve the antimicrobial activities against multidrug resistant bacteria. creator: Deepan Gautam creator: Karma Gurmey Dolma creator: Bidita Khandelwal creator: Madhu Gupta creator: Meghna Singh creator: Tooba Mahboob creator: Anil Teotia creator: Prasad Thota creator: Jaydeep Bhattacharya creator: Ramesh Goyal creator: Sonia M.R. Oliveira creator: Maria de Lourdes Pereira creator: Christophe Wiart creator: Polrat Wilairatana creator: Komgrit Eawsakul creator: Mohammed Rahmatullah creator: Shanmuga Sundar Saravanabhavan creator: Veeranoot Nissapatorn uri: https://doi.org/10.7717/peerj.15590 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gautam et al. title: Large-sized fossil hamsters from the late Middle Pleistocene Locality 2 of Shanyangzhai, China, and discussion on the validity of Cricetinus and C. varians (Rodentia: Cricetidae) link: https://peerj.com/articles/15604 last-modified: 2023-07-28 description: A detailed morphological description and comparative study were conducted on numerous large-sized hamster remains collected from the late Middle Pleistocene Locality 2 of Shanyangzhai (Syz 2), Hebei Province, China. The comparisons reveal that these fossils are highly similar to the extant Tscherskia triton in size and morphology, including the small degree of alternating between the main opposite cusps on M1-3, the presence of axioloph on M3, and mesolophids on m1-2 that are present but seldom reach the lingual margin of the teeth, among other features. However, minor differences between the two still exist. Consequently, all these fossils are designated as a chronosubspecies of the extant species, T. triton varians comb. nov. The skull and molar morphologies of Cricetinus varians and T. triton were meticulously compared to resolve the long-standing debate regarding the validity of Cricetinus Zdansky, 1928 and C. varians Zdansky, 1928. The findings indicate that the differences between the two are slight; as a result, C. varians can only be considered a chronosubspecies of T. triton, i.e., T. triton varians comb. nov., and Cricetinus should be recognized as a junior synonym of Tscherskia. We tentatively propose that, among the seven species once referred to Cricetinus, C. europaeus, C. gritzai, C. janossyi, and C. koufosi should be reassigned to Tscherskia, while C. beremendensis should be transferred to Allocricetus, and C. mesolophidos to Neocricetodon. Excluding Tscherskia sp. from the Late Pliocene Youhe fauna, there are no reliable Tscherskia fossils in China earlier than the Middle Pleistocene. Based on the current evidence, Tscherskia may have originated from Neocricetodon during the Early Pliocene in Europe and subsequently spread to Asia. T. triton is its sole surviving representative, which now exclusively inhabits East Asia. creator: Kun Xie creator: Yunxiang Zhang creator: Yongxiang Li uri: https://doi.org/10.7717/peerj.15604 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Xie et al.