title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=374 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Cloning and functional characterization of porcine AACS revealing the regulative roles for fat deposition in pigs link: https://peerj.com/articles/16406 last-modified: 2023-11-20 description: Fat deposition is a quantitative trait controlled by multiple genes in pigs. Using transcriptome sequencing, we previously reported that AACS is differentially expressed in the subcutaneous fat tissue of Dingyuan pigs with divergent backfat thickness. Therefore, with the aim of further characterizing this gene and its protein, we cloned the entire 3286-bp mRNA sequence of the porcine AACS, and the encoded AACS protein is a hydrophilic protein without a signal peptide or transmembrane sequence. Our findings suggested that among various tissues and pig breeds, AACS was highly expressed in subcutaneous fat. We have identified three completely linked SNP loci in the AACS gene: A-1759C, C-1683T, and A-1664G. The double luciferase activity test in the 5′ flanking region indicated that the flanking region of AACS contained several active regulatory elements. The three linked SNPs that were identified in one of the critical active elements, and might serve as important molecular markers regulating backfat thickness. Finally, we observed that AACS overexpression inhibited the proliferation and differentiation of subcutaneous preadipocytes. Collectively, our results suggest that AACS inhibits subcutaneous fat deposition in pigs. This study provides a new molecular marker for understanding the mechanism of porcine fat deposition. creator: Pan Zhang creator: Bo Zhang creator: Yu Fu creator: Pan Li creator: Hao Zhang uri: https://doi.org/10.7717/peerj.16406 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Quantifying the land and population risk of sewage spills overland using a fine-scale, DEM-based GIS model link: https://peerj.com/articles/16429 last-modified: 2023-11-20 description: Accidental releases of untreated sewage into the environment, known as sewage spills, may cause adverse gastrointestinal stress to exposed populations, especially in young, elderly, or immune-compromised individuals. In addition to human pathogens, untreated sewage contains high levels of micropollutants, organic matter, nitrogen, and phosphorus, potentially resulting in aquatic ecosystem impacts such as algal blooms, depleted oxygen, and fish kills in spill-impacted waterways. Our Geographic Information System (GIS) model, Spill Footprint Exposure Risk (SFER) integrates fine-scale elevation data (1/3 arc-second) with flowpath tracing methods to estimate the expected overland pathways of sewage spills and the locations where they are likely to pool. The SFER model can be integrated with secondary measures tailored to the unique needs of decision-makers so they can assess spatially potential exposure risk. To illustrate avenues to assess risk, we developed risk measures for land and population health. The land risk of sewage spills is calculated for subwatershed regions by computing the proportion of the subwatershed’s area that is affected by one modeled footprint. The population health risk is assessed by computing the estimated number of individuals who are within the modeled footprint using fine-scale (90 square meters) population estimates data from LandScan USA. In the results, with a focus on the Atlanta metropolitan region, potential strategies to combine these risk measures with the SFER model are outlined to identify specific areas for intervention. creator: Emma L. McDaniel creator: Samuel F. Atkinson creator: Chetan Tiwari uri: https://doi.org/10.7717/peerj.16429 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 McDaniel et al. title: Insight from the association between critical thinking and English argumentative writing: catering to English learners’ writing ability link: https://peerj.com/articles/16435 last-modified: 2023-11-20 description: IntroductionEnglish argumentative writing (EAW) is a ‘problem-solving’ cognitive process, and its relationship with critical thinking has drawn attention in China. This is because fostering EAW proficiency is a crucial element but a challenging task for Chinese high school English teaching and learning. The present study examined how critical thinking is related to Chinese high school students’ EAW performance. The study identified eight critical thinking disposition (CTD) subscales and aims to determine whether EAW and CTD are correlated.MethodsA questionnaire modified from the Chinese Version Critical Thinking Disposition Inventory (CTDI-CV) and the Evaluation Criteria for English Argumentative Writing (ECEAW) were employed in this study. Both instruments were administered to 156 students from Grade 12. A purposive sampling of high school students was used in this study. Student EAW performance was scored by two experts based on the Evaluation Criteria for English Argumentative Writing.ResultsA significant relationship was found between students’ CTD and EAW abilities. Furthermore, among the eight CTD subdispositions, cognitive maturity, truth-seeking, analyticity, and justice were found to be positively correlated with EAW, and they all were found to be the main predictors of EAW proficiency among high school students.ConclusionZhangzhou high school students’ CTDs were overall positive, and students’ EAW performance correlated significantly with the overall CTD and its four subdispositions of cognitive maturity, truth-seeking, analyticity, and justice. These four subdispositions showed a significantly predictive validity on EAW performance as well. creator: Yanfang Hu creator: Atif Saleem uri: https://doi.org/10.7717/peerj.16435 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Hu and Saleem title: Genome-wide identification of 2-oxoglutarate and Fe (II)-dependent dioxygenase family genes and their expression profiling under drought and salt stress in potato link: https://peerj.com/articles/16449 last-modified: 2023-11-20 description: The 2-Oxoglutatrate-dependent dioxygenases (2OGDs) comprise the 2-Oxoglutatrate and Fe(II)-dependent dioxygenases (2ODD) enzyme families that facilitate the biosynthesis of various compounds like gibberellin, ethylene, etc. The 2OGDs are also involved in various catabolism pathways, such as auxin and salicylic acid catabolism. Despite their important roles, 2ODDs have not been studied in potato, which is the third most important crop globally. In this study, a comprehensive genome wide analysis was done to identify all 2ODDs in potatoes, and the putative genes were analysed for the presence of the signature 2OG-FeII_Oxy (PF03171) domain and the conserved DIOX_N (PF14226) domain. A total of 205 St2ODDs were identified and classified into eight groups based on their function. The physiochemical properties, gene structures, and motifs were analysed, and gene duplication events were also searched for St2ODDs. The active amino acid residues responsible for binding with 2-oxoglutarate and Fe (II) were conserved throughout the St2ODDs. The three-dimensional (3D) structures of the representative members of flavanol synthase (FNS), 1-aminocyclopropane-1-carboxylic acid oxidases (ACOs), and gibberellin oxidases (GAOXs) were made and docked with their respective substrates, and the potential interactions were visualised. The expression patterns of the St2ODDs under abiotic stressors such as heat, salt, and drought were also analysed. We found altered expression levels of St2ODDs under abiotic stress conditions, which was further confirmed for drought and salt stress using qRT-PCR. The expression levels of St2ODD115, St2ODD34, and St2ODD99 were found to be upregulated in drought stress with 2.2, 1.8, and 2.6 fold changes, respectively. After rewatering, the expression levels were normal. In salt stress, the expression levels of St2ODD151, St2ODD76, St2ODD91, and St2ODD34 were found to be upregulated after 24 hours (h), 48 hours (h), 72 hours (h), and 96 hours (h). Altogether, the elevated expression levels suggest the importance of St2ODDs under abiotic stresses, i.e., drought and salt. Overall, our study provided a knowledge base for the 2ODD gene family in potato, which can be used further to study the important roles of 2ODDs in potato plants. creator: Hanny Chauhan creator: Aiana creator: Kashmir Singh uri: https://doi.org/10.7717/peerj.16449 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Chauhan et al. title: Self-control mediates the relationship between time perspective and mobile phone addiction in Chinese college students link: https://peerj.com/articles/16467 last-modified: 2023-11-20 description: BackgroundMobile phone addiction (MPA) is a prevalent problem among college students, and Chinese college students are a high-risk group for smartphone addiction. MPA has a negative impact on the physical and mental health and academic performance of college students. Studies have explored the influence of many factors on MPA, such as the characteristics of the smartphone itself, the characteristics of the smartphone user, and the environment. However, to date, no studies have explored the protective and risk factors for MPA from the perspective of personality traits. From this perspective, this study explored the influence of time perspective and trait self-control on MPA to identify effective measures to prevent and intervene in MPA in college students.MethodsThe participants in this cross-sectional study were 526 Chinese college students. They completed the Zimbardo Time Perspective Inventory, the Self-Control Scale and the Mobile Phone Addiction Tendency Scale using an online questionnaire tool. Pearson correlation analysis was used to explore the relationships among time perspective, self-control and MPA. A latent variable mediation analysis of the structural equation model was used to examine the mediating role of self-control in the relationship between time perspective and MPA.ResultsVarious dimensions of time perspective were strongly associated with MPA. Among these dimensions, past negative (r = 0.397, p < 0.001), present hedonistic (r = 0.207, p < 0.001), and present fatalistic perspectives (r = 0.444, p < 0.001) were positively associated with MPA, while a future time perspective (r = −0.200, p < 0.001) was negatively associated with MPA. Mediation effects analysis showed that past negative (β = 0.034, p < 0.001, 95% CI [0.020–0.051]), present hedonistic (β = 0.038, p < 0.001, 95% CI [0.02–0.06]), present fatalistic (β = 0.047, p < 0.001, 95% CI [0.031–0.065]) and future orientation perspectives (β = −0.093, p < 0.001, 95% CI [−0.123–0.069]) indirectly influenced MPA through the mediating effect of self-control.ConclusionThis study confirmed that a future time perspective and self-control are protective factors for MPA and that past negative, present hedonistic and present fatalistic perspectives are risk factors for MPA. College educators can prevent MPA in college students directly by cultivating their self-control ability, as well as indirectly by increasing their use of future time perspective and reducing past negative, present fatalistic and present hedonistic perspectives. creator: Weigang Pan creator: Yingzhi Ma creator: Yihong Long creator: Ying Wang creator: Yujie Zhao uri: https://doi.org/10.7717/peerj.16467 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Pan et al. title: Minimally invasive pyeloplasty versus open pyeloplasty for ureteropelvic junction obstruction in infants: a systematic review and meta-analysis link: https://peerj.com/articles/16468 last-modified: 2023-11-20 description: BackgroundTo compare the perioperative outcomes and success rates of minimally invasive pyeloplasty (MIP), including laparoscopic and robotic-assisted laparoscopic pyeloplasty, with open pyeloplasty (OP) in infants.Materials and MethodsIn September 2022, a systematic search of PubMed, EMBASE, and the Cochrane Library databases was undertaken. The systematic review and meta-analysis were conducted in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, with the study registered prospectively in the PROSPERO database (CRD42022359475).ResultsEleven studies were included. Dichotomous and continuous variables were presented as odds ratios (OR) and standard mean differences (SMD), respectively, with their 95% confidence intervals (CI). Compared to OP, a longer operation time and shorter length of stay were associated with MIP (SMD: 0.96,95% CI: 0.30 to 1.62, p = 0.004, and SMD: −1.12, 95% CI: −1.82 to −0.43, p = 0.002, respectively). No significant differences were found between the MIP and OP in terms of overall postoperative complications (OR:0.84, 95% CI: 0.52 to 1.35, p = 0.47), minor complications (OR: 0.76, 95% CI: 0.40 to 1.42, p = 0.39), or major complications (OR: 1.10, 95% CI: 0.49 to 2.50, p = 0.81). In addition, a lower stent placement rate was related to MIP (OR: 0.09, 95% CI: 0.02 to 0.47, p = 0.004). There was no statistical difference for success rate between the MIP and OP (OR: 1.35, 95% CI: 0.59 to 3.07, p = 0.47). Finally, the results of subgroup analysis were consistent with the above.ConclusionsOur meta-analysis demonstrates that MIP is a feasible and safe alternative to OP for infants, presenting comparable perioperative outcomes and similar success rates, albeit requiring longer operation times. However, it is essential to consider the limitations of our study, including the inclusion of studies with small sample sizes and the combination of both prospective and retrospective research designs. creator: Min Wang creator: Yu Xi creator: Nanxiang Huang creator: Pengli Wang creator: Li Zhang creator: Mingjia Zhao creator: Siyi Pu uri: https://doi.org/10.7717/peerj.16468 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Long-term toxicity of chlorpromazine, diclofenac and two lanthanides on three generations of Ceriodaphnia dubia link: https://peerj.com/articles/16472 last-modified: 2023-11-20 description: Amultigenerational study on Ceriodaphnia dubia was carried out by exposing three subsequent generations to pharmaceuticals chlorpromazine (CPZ) and diclofenac (DCF), and two lanthanide chlorides, gadolinium as GdCl3 and europium as EuCl3. As the treatments, environmentally relevant concentrations were chosen (0.001, 0.01 and 0.1 mg/L for CPZ; 0.1, 1 and 10 mg/L for DCF; 0.425, 4.25 and 42.5 µg/L for Gd and 0.41, 4.1 and 41 µg/L for Eu). Survival, population growth and reproduction success were evaluated at 21 and 30 days of exposure, and the whole observation period lasted 40 days. The least sensitive to all selected substances was the first daphnid generation (F1). Within 21-day exposure, no significant effects of the psychotropic drug CPZ on C. dubia survival were observed in generations F1–F3. The anti-inflammatory drug DCF did not affect survival in the F1 generation; however, it significantly reduced survival in the F3 generation at 1–10 mg/L. Both lanthanides did not affect survival in the F1 and F2 generations of C. dubia but considerably decreased survival in the F3 at 4–42 µg/L. Both pharmaceuticals stimulated the reproduction of C. dubia in the F1 generation, while inhibition occurred at the highest tested concentrations in generations F2 and F3. The inhibitory effect on the reproductive success of lanthanides in the F2 generation resembled that for CPZ but not for DCF. The dynamics of adverse effects during the 21–30-day period revealed that despite increased mortality in the controls (up to 30%), concentrations used in the study minified, in most instances, the survival and aggravated population growth and reproduction success of C. dubia. Our data suggest that C. dubia as a test organism can be used for 21 days in multigenerational investigations, especially when testing close to environmental concentrations. In this respect, the standard C. dubia chronic toxicity assay seems limited since prolonged observations and several generations of daphnids are required to obtain reliable information for the risk assessment of potentially aggressive chemicals. creator: Brigita Gylytė creator: Viktoria Martinyuk creator: Reda Cimmperman creator: Rolandas Karitonas creator: Oksana Stoliar creator: Levonas Manusadžianas uri: https://doi.org/10.7717/peerj.16472 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Gylytė et al. title: Factors affecting the relative abundance in an overfished stock: red grouper (Epinephelus morio) in the Southeastern Gulf of Mexico link: https://peerj.com/articles/16490 last-modified: 2023-11-20 description: The most important fisheries are recording catches below their historical averages despite increased effort. This level of overfishing is worrying and requires the establishment of feasible and precise measures to prevent a continuing decrease in biomass. Determining the factors that lead to changes in the abundance and distribution of overfished resources would allow us to identify the strengths and weaknesses of management schemes; this approach would also make it possible to estimate more accurate parameters for their evaluation. We hypothesize that environmental, temporal, spatial, and operational components contribute to the variation in the relative abundance. Thus, we analyzed the red grouper fishery, the most important demersal fishery in the southeastern Gulf of Mexico (SGM); it is locally known as escama. We employed the catch per unit effort (CPUE) as an index of relative abundance recorded by the semi-industrial fleet (kilogram per effective fishing day) and the small-scale fleet (kilogram per effective fishing hour) during the overexploitation phase (from 1996 to 2019). We fitted several variables of the components using generalized additive models (GAM) and used multi-model inference to determine the best GAM for each fleet. For both fleets, the operational and temporal components (fishing gear and year) have had a greater impact on the distribution and abundance of red grouper in the SGM than the spatial and environmental components (the place of origin and sea surface temperature). These findings encourage the exploration of métier schemes for more efficient fishery management. In addition, we have identified several strategies that would support the recovery of the resource, such as restricting fishing in the quadrants located to the northeast or regulating scuba diving. We recommend that in the future, researchers use the indices we have generated in the present study to evaluate the red grouper fishery. creator: Iván Oribe-Pérez creator: Iván Velázquez-Abunader creator: Carmen Monroy-García uri: https://doi.org/10.7717/peerj.16490 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Oribe-Pérez et al. title: TMUB1 expression is associated with the prognosis of colon cancer and immune cell infiltration link: https://peerj.com/articles/16334 last-modified: 2023-11-17 description: BackgroundTMUB1 is a transmembrane protein involved in biological signaling and plays an important role in the stability and transcription of P53. However, its role in tumor remains unknown.MethodsUsing R language, the expression level of 33 cancer spectrum TMUB1 was analyzed by the public database TCGA, GEO and HPA, the differential expressed gene (DEG) screening and protein interaction (PPI) network was constructed, and the differential genes of TMUB1 in colon cancer were identified. The relevant signaling pathways were identified by gene functional annotation and enrichment analysis. The ssGSEA algorithm in GSVA were used for immune infiltration analysis. The Kaplan-Meier analysis, univariate and multivariate Cox regression analysis, nomogram and calibration map analysis were constructed to evaluate the correlation between TMUB1 expression and clinical prognosis. The expression levels of TMUB1 in intestinal cancer cell lines as well as in 10 intestinal cancer tissues were verified by qPCR experiments.ResultsThrough the bioinformatics analysis of multiple databases and preliminary experimental studies, we found that the expression of TMUB1 was significantly increased in colon cancer tumors, and was correlated with the clinical N stage, pathological grade, lymphatic metastasis and BMI of colon cancer. TMUB1 may be involved in the regulation of the malignant progression of colon cancer. Meanwhile, patients with high expression of TMUB1 mRNA had worse OS and DSS, and TMUB1 expression was an independent prognostic factor for OS and DSS. It was further found that highly expressed TMUB1 tissues showed low levels of immune infiltration and stromal infiltration.ConclusionWe reported the expression level of TMUB1 in colon cancer and analyzed its potential prognostic value in colon cancer through the bioinformatics analysis and preliminary experimental studies. The high expression of TMUB1 is a negative prognostic factor for colon cancer patients. TMUB1 may be a potential target for colon cancer. creator: Yan Lu creator: Kang Wang creator: Yuanhong Peng creator: Jun Zhang creator: Qinuo Ju creator: Qihuan Xu creator: Manzhao Ouyang creator: Zhiwei He uri: https://doi.org/10.7717/peerj.16334 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lu et al. title: Microbes within the building envelope—a case study on the patterns of colonization and potential sampling bias link: https://peerj.com/articles/16355 last-modified: 2023-11-17 description: Humans are exposed to diverse communities of microbes every day. With more time spent indoors by humans, investigations into the communities of microbes inhabiting occupied spaces have become important to deduce the impacts of these microbes on human health and building health. Studies so far have given considerable insight into the communities of the indoor microbiota humans interact with, but mainly focus on sampling surfaces or indoor dust from filters. Beneath the surfaces though, building envelopes have the potential to contain environments that would support the growth of microbial communities. But due to design choices and distance from ground moisture, for example, the temperature and humidity across a building will vary and cause environmental gradients. These microenvironments could then influence the composition of the microbial communities within the walls. Here we present a case study designed to quantify any patterns in the compositions of fungal and bacterial communities existing in a building envelope and determine some of the key variables, such as cardinal direction, distance from floor or distance from wall joinings, that may influence any microbial community composition variation. By drilling small holes across walls of a house, we extracted microbes onto air filters and conducted amplicon sequencing. We found sampling height (distance from the floor) and cardinal direction the wall was facing caused differences in the diversity of the microbial communities, showing that patterns in the microbial composition will be dependent on sampling location within the building. By sampling beneath the surfaces, our approach provides a more complete picture of the microbial condition of a building environment, with the significant variation in community composition demonstrating a potential sampling bias if multiple sampling locations across a building are not considered. By identifying features of the built environment that promote/retard microbial growth, improvements to building designs can be made to achieve overall healthier occupied spaces. creator: Lucy R. Davies creator: Aitor Barbero-López creator: Veli-Matti Lähteenmäki creator: Antti Salonen creator: Filip Fedorik creator: Antti Haapala creator: Phillip C. Watts uri: https://doi.org/10.7717/peerj.16355 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Davies et al.