title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=399 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Theoretical study of ArcB and its dimerization, interaction with anaerobic metabolites, and activation of ArcA link: https://peerj.com/articles/16309 last-modified: 2023-10-13 description: The complex metabolism of Escherichia coli has been extensively studied, including its response to oxygen availability. The ArcA/B two-component system (TCS) is the key regulator for the transition between these two environmental conditions and has been thoroughly characterized using genetic and biochemical approaches. Still, to date, limited structural data is available. The breakthrough provided by AlphaFold2 in 2021 has brought a reliable tool to the scientific community for assessing the structural features of complex proteins. In this report, we analyzed the structural aspects of the ArcA/B TCS using AlphaFold2 models. The models are consistent with the experimentally determined structures of ArcB kinase. The predicted structure of the dimeric form of ArcB is consistent with the extensive genetic and biochemical data available regarding mechanistic signal perception and regulation. The predicted interaction of the dimeric form of ArcB with its cognate response regulator (ArcA) is also consistent with both the forward and reverse phosphotransfer mechanisms. The ArcB model was used to detect putative binding cavities to anaerobic metabolites, encouraging testing of these predictions experimentally. Finally, the highly accurate models of other ArcB homologs suggest that different experimental approaches are needed to determine signal perception in kinases lacking the PAS domain. Overall, ArcB is a kinase with features that need further testing, especially in determining its crystal structure under different conditions. creator: Felipe Padilla-Vaca creator: Javier de la Mora creator: Rodolfo García-Contreras creator: Jorge Humberto Ramírez-Prado creator: Marcos Vicente-Gómez creator: Francisco Vargas-Gasca creator: Fernando Anaya-Velázquez creator: Itzel Páramo-Pérez creator: Ángeles Rangel-Serrano creator: Patricia Cuéllar-Mata creator: Naurú Idalia Vargas-Maya creator: Bernardo Franco uri: https://doi.org/10.7717/peerj.16309 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Padilla-Vaca et al. title: Microbiota composition and correlations with environmental factors in grass carp (Ctenopharyngodon idella) culture ponds in South China link: https://peerj.com/articles/15892 last-modified: 2023-10-12 description: To maintain the health of aquaculture fish, it is critical to understand the composition of microorganisms in aquaculture water and sediment and the factors affecting them. This study examined the water and sediment microbiota compositions of four different types of ponds in South China that were used to culture grass carp (Ctenopharyngodon idella) of different sizes through high-throughput sequencing of the 16S rRNA gene, and analyzed their correlations with environmental factors. The results showed that ponds with cultured grass carp of different sizes exhibited significant differences in terms of water physicochemical properties and composition of water and sediment microbiota. Furthermore, the exchange of microorganisms between water and sediment microbiota was lowest in ponds with the smallest grass carp and highest in ponds with the largest grass carp. All detected environmental factors except water temperature were significantly correlated with the water microbiota, and all detected environmental factors in the sediment were correlated with sediment microbiota. Moreover, Aeromonas hydrophila and Vibrio were significantly increased in the water microbiota, especially in ponds with small juvenile grass carp, implying an increased risk of A. hydrophila and Vibrio infections in these environments. Our results provide useful information for the management of grass carp aquaculture ponds. creator: Yingli Lian creator: Xiafei Zheng creator: Shouqi Xie creator: Dan A creator: Jian Wang creator: Jiayi Tang creator: Xuan Zhu creator: Baojun Shi uri: https://doi.org/10.7717/peerj.15892 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lian et al. title: Towards a scientific community consensus on designating Vulnerable Marine Ecosystems from imagery link: https://peerj.com/articles/16024 last-modified: 2023-10-12 description: Management of deep-sea fisheries in areas beyond national jurisdiction by Regional Fisheries Management Organizations/Arrangements (RFMO/As) requires identification of areas with Vulnerable Marine Ecosystems (VMEs). Currently, fisheries data, including trawl and longline bycatch data, are used by many RFMO/As to inform the identification of VMEs. However, the collection of such data creates impacts and there is a need to collect non-invasive data for VME identification and monitoring purposes. Imagery data from scientific surveys satisfies this requirement, but there currently is no established framework for identifying VMEs from images. Thus, the goal of this study was to bring together a large international team to determine current VME assessment protocols and establish preliminary global consensus guidelines for identifying VMEs from images. An initial assessment showed a lack of consistency among RFMO/A regions regarding what is considered a VME indicator taxon, and hence variability in how VMEs might be defined. In certain cases, experts agreed that a VME could be identified from a single image, most often in areas of scleractinian reefs, dense octocoral gardens, multiple VME species’ co-occurrence, and chemosynthetic ecosystems. A decision flow chart is presented that gives practical interpretation of the FAO criteria for single images. To further evaluate steps of the flow chart related to density, data were compiled to assess whether scientists perceived similar density thresholds across regions. The range of observed densities and the density values considered to be VMEs varied considerably by taxon, but in many cases, there was a statistical difference in what experts considered to be a VME compared to images not considered a VME. Further work is required to develop an areal extent index, to include a measure of confidence, and to increase our understanding of what levels of density and diversity correspond to key ecosystem functions for VME indicator taxa. Based on our results, the following recommendations are made: 1. There is a need to establish a global consensus on which taxa are VME indicators. 2. RFMO/As should consider adopting guidelines that use imagery surveys as an alternative (or complement) to using bycatch and trawl surveys for designating VMEs. 3. Imagery surveys should also be included in Impact Assessments. And 4. All industries that impact the seafloor, not just fisheries, should use imagery surveys to detect and identify VMEs. creator: Amy R. Baco creator: Rebecca Ross creator: Franziska Althaus creator: Diva Amon creator: Amelia E. H. Bridges creator: Saskia Brix creator: Pål Buhl-Mortensen creator: Ana Colaco creator: Marina Carreiro-Silva creator: Malcolm R. Clark creator: Cherisse Du Preez creator: Mari-Lise Franken creator: Matthew Gianni creator: Genoveva Gonzalez-Mirelis creator: Thomas Hourigan creator: Kerry Howell creator: Lisa A. Levin creator: Dhugal J. Lindsay creator: Tina N. Molodtsova creator: Nicole Morgan creator: Telmo Morato creator: Beatriz E. Mejia-Mercado creator: David O’Sullivan creator: Tabitha Pearman creator: David Price creator: Katleen Robert creator: Laura Robson creator: Ashley A. Rowden creator: James Taylor creator: Michelle Taylor creator: Lissette Victorero creator: Les Watling creator: Alan Williams creator: Joana R. Xavier creator: Chris Yesson uri: https://doi.org/10.7717/peerj.16024 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Baco et al. title: Diurnal predators of restocked lab-reared and wild Diadema antillarum near artificial reefs in Saba link: https://peerj.com/articles/16189 last-modified: 2023-10-12 description: The long-spined sea urchin Diadema antillarum controls reef dynamics by grazing on algae and increasing coral recruitment. Populations of Diadema never recovered after a mass-die off in 1983 and 1984, and numbers were further reduced by a more recent die-off in 2022. To restore grazing pressure and thereby the resilience of Caribbean coral reefs, multiple Diadema restocking efforts have been performed. Although results vary, relatively low retention is one of the reasons restocking is not considered more often. If causes for the low retention can be identified, suitable measures may be able to increase restocking success. In this study, we monitored restocked lab-reared and wild juvenile Diadema on artificial reefs around Saba, Caribbean Netherlands. To assess the retention of Diadema over time, we conducted diver surveys and used underwater photo time lapse during daylight. Retention of uncaged lab-reared and wild Diadema decreased steadily with less than 30% surviving after 10 days. In total, 138 predator-prey interactions were recorded, of which 99% involved the queen triggerfish Balistes vetula, although other potential predators were present in the area. None of the recorded predator-prey interactions was successful, which suggests that artificial reefs with incorporated shelters may be suitable for juveniles as daytime refuge. However, Diadema that were more often attacked during the day were more likely to be absent the next morning. Because queen triggerfish often visited the experimental site in the first or last hour of daylight, it could be that they were more successful in their attacks when it was too dark to see anything on the photos and when Diadema came out to feed or to look for better shelter opportunities. If Diadema migrated off the artificial reef, they were probably predated during the process, because no Diadema were found on surrounding reefs. Wild Diadema were attacked significantly more often than lab-reared Diadema, possibly because the wild urchins were larger, but this did not significantly affect retention. Future restocking should be performed on natural or artificial reefs with deeper shelters, so Diadema can retract farther into their crevice, and should include night-time monitoring to identify the remaining unknown factors that cause low retention, including migration and nocturnal predation. This knowledge is urgently needed to coral reef managers so they can increase Diadema restocking success by selecting reefs with a lower predator density, protect urchins during an acclimatization period and/or conduct temporary predator control measures. creator: Mareike de Breuyn creator: Alex J. van der Last creator: Oliver J. Klokman creator: Alwin Hylkema uri: https://doi.org/10.7717/peerj.16189 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 de Breuyn et al. title: Cuproptosis-related lncRNA SNHG16 as a biomarker for the diagnosis and prognosis of head and neck squamous cell carcinoma link: https://peerj.com/articles/16197 last-modified: 2023-10-12 description: BackgroundWe aim to investigate the potential value of cuproptosis-related lncRNA signaling in predicting clinical prognosis and immunotherapy and its relationship with drug sensitivity in head and neck squamous cell carcinoma (HNSCC).MethodsWe first identified the lncRNAs associated with cuproptosis genes in HNSCC and then conducted a series of analytical studies to investigate the expression and prognostic significance of these lncRNAs. Finally, we used RT-qPCR to validate our findings in a laryngeal squamous cell carcinoma cell line and 12 pairs of laryngeal squamous cell carcinoma and adjacent normal tissues.ResultsWe identified 11 differentially expressed lncRNAs that were associated with cuproptosis genes in HNSCC and also served as prognostic markers for this cancer. Enrichment analysis revealed that these lncRNAs were related to immune-related functions that were suppressed in patients with oncogene mutations in the high-risk group. The patients with a high tumor mutation burden exhibited poor overall survival (OS). We used the tumor immune dysfunction and exclusion model to show that the patients in the high-risk group had great potential for immune evasion and less effective immunotherapy. We also identified several drugs that could be effective in treating HNSCC. Experimental validation showed that AC090587.1 and AC012184.3 exhibited differential expression between the TU686 and HBE cell lines, and SNHG16 showed differential expression among the TU686, TU212, and control HBE cells. Among the 12 pairs of cancer and adjacent tissues collected in the clinic, only SNHG16 showed differential expression. Targeted therapy against SNHG16 holds promise as a prospective novel strategy for the clinical management of HNSCC. creator: Baoai Han creator: Shuang Li creator: Shuo Huang creator: Jing Huang creator: Tingting Wu creator: Xiong Chen uri: https://doi.org/10.7717/peerj.16197 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Han et al. title: An application of topological data analysis in predicting sumoylation sites link: https://peerj.com/articles/16204 last-modified: 2023-10-12 description: Sumoylation is a reversible post-translational modification that regulates certain significant biochemical functions in proteins. The protein alterations caused by sumoylation are associated with the incidence of some human diseases. Therefore, identifying the sites of sumoylation in proteins may provide a direction for mechanistic research and drug development. Here, we propose a new computational approach for identifying sumoylation sites using an encoding method based on topological data analysis. The features of our model captured the key physical and biological properties of proteins at multiple scales. In a 10-fold cross validation, the outcomes of our model showed 96.45% of sensitivity (Sn), 94.65% of accuracy (Acc), 0.8946 of Matthew’s correlation coefficient (MCC), and 0.99 of area under curve (AUC). The proposed predictor with only topological features achieves the best MCC and AUC in comparison to the other released methods. Our results suggest that topological information is an additional parameter that can assist in the prediction of sumoylation sites and provide a novel perspective for further research in protein sumoylation. creator: Xiaoxi Lin creator: Yaru Gao creator: Fengchun Lei uri: https://doi.org/10.7717/peerj.16204 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lin et al. title: Nomogram model for predicting the risk of post-stroke depression based on clinical characteristics and DNA methylation link: https://peerj.com/articles/16240 last-modified: 2023-10-12 description: ObjectiveTo construct a comprehensive nomogram model for predicting the risk of post-stroke depression (PSD) by using clinical data that are easily collected in the early stages, and the level of DNA methylation, so as to help doctors and patients prevent the occurrence of PSD as soon as possible.MethodsWe continuously recruited 226 patients with a history of acute ischemic stroke and followed up for three months. Socio-demographic indicators, vascular-risk factors, and clinical data were collected at admission, and the outcome of depression was evaluated at the third month after stroke. At the same time, a DNA-methylation-related sequencing test was performed on the fasting peripheral blood of the hospitalized patients which was taken the morning after admission.ResultsA total of 206 samples were randomly divided into training dataset and validation set according to the ratio of 7:3. We screened 24 potentially-predictive factors by Univariate logistic regression and least absolute shrinkage and selection operator (LASSO) regression analysis, and 10 of the factors were found to have predictive ability in the training set. The PSD nomogram model was established based on seven significant variables in multivariate logistic regression. The consistency statistic (C-index) was as high as 0.937, and the area under curve (AUC) in the ROC analysis was 0.933. Replication analysis results in the validation set suggest the C-index was 0.953 and AUC was 0.926. This shows that the model has excellent calibration and differentiating abilities.ConclusionGender, Rankin score, history of hyperlipidemia, time from onset to hospitalization, location of stroke, National Institutes of Health Stroke scale (NIHSS) score, and the methylation level of the cg02550950 site are all related to the occurrence of PSD. Using this information, we developed a prediction model based on methylation characteristics. creator: Shihang Luo creator: Fan Liu creator: Qiao Liao creator: Hengshu Chen creator: Tongtong Zhang creator: Rui Mao uri: https://doi.org/10.7717/peerj.16240 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Luo et al. title: Spatial effects of trade, foreign direct investment (FDI), and natural resource rents on carbon productivity in the GCC region link: https://peerj.com/articles/16281 last-modified: 2023-10-12 description: BackgroundNatural resource rents (NRRs) may determine the environment and economic growth of the GCC countries due to their over-reliance on the natural resource sector. NRRs are the source of income in resource-abundant GCC countries. So, increasing income of these countries could pollute the environment by increasing overall economic activities. Consequently, NRRs could determine carbon productivity in the GCC region through increasing income and carbon emissions.MethodsThe effects of trade openness (TO), foreign direct investment (FDI), urbanization, and oil and natural gas rents on carbon productivity (CP) are examined in the GCC region from 1980–2021 using the spatial Durbin model.ResultsThe CP of the GCC countries has spillovers in their neighboring countries. Oil rent reduces carbon productivity in domestic economies and the entire GCC region. Natural gas rent, TO, and FDI increase, and urbanization reduces carbon productivity in neighboring economies and the entire GCC region. Moreover, urbanization reduces carbon productivity in domestic economies as well. The study recommends the GCC countries to reduce reliance on oil rent and increase globalization in terms of TO and FDI in the region to promote carbon productivity. Moreover, GCC countries should also focus more on natural gas rent instead of oil rent to raise carbon productivity. creator: Haider Mahmood uri: https://doi.org/10.7717/peerj.16281 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mahmood title: Prognostic analyses of genes associated with anoikis in breast cancer link: https://peerj.com/articles/15475 last-modified: 2023-10-11 description: Breast cancer (BRCA) is the most diagnosed cancer worldwide and is responsible for the highest cancer-associated mortality among women. It is evident that anoikis resistance contributes to tumour cell metastasis, and this is the primary cause of treatment failure for BRCA. However, anoikis-related gene (ARG) expression profiles and their prognostic value in BRCA remain unclear. In this study, a prognostic model of ARGs based on The Cancer Genome Atlas (TCGA) database was established using a least absolute shrinkage and selection operator analysis to evaluate the prognostic value of ARGs in BRCA. The risk factor graph demonstrated that the low-risk group had longer survival than the high-risk group, implying that the prognostic model had a good performance. We identified 11 ARGs that exhibited differential expression between the two risk groups in TCGA and Gene Expression Omnibus databases. Through Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes enrichment analyses, we revealed that the screened ARGs were associated with tumour progression and metastasis. In addition, a protein–protein interaction network showed potential interactions among these ARGs. Furthermore, gene set enrichment analysis suggested that the Notch and Wnt signalling pathways were overexpressed in the high-risk group, and gene set variation analysis revealed that 38 hallmark genes differed between the two groups. Moreover, Kaplan–Meier survival curves and receiver operating characteristic curves were used to identify five ARGs (CD24, KRT15, MIA, NDRG1, TP63), and quantitative polymerase chain reaction was employed to assess the differential expression of these ARGs. Univariate and multivariate Cox regression analyses were then performed for the key ARGs, with the best prediction of 3 year survival. In conclusion, ARGs might play a crucial role in tumour progression and serve as indicators of prognosis in BRCA. creator: Jingyu Cao creator: Xinyi Ma creator: Guijuan Zhang creator: Shouyi Hong creator: Ruirui Ma creator: Yanqiu Wang creator: Xianxin Yan creator: Min Ma uri: https://doi.org/10.7717/peerj.15475 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cao et al. title: Evaluation of drought stress level in Sargent’s cherry (Prunus sargentii Rehder) using photosynthesis and chlorophyll fluorescence parameters and proline content analysis link: https://peerj.com/articles/15954 last-modified: 2023-10-11 description: Sargent’s cherry trees (Prunus sargentiiRehder) are widely planted as an ornamental, climate change-sensing species. This study investigated changes in the soil moisture content, fresh weight, photosynthesis and chlorophyll fluorescence properties, and the chlorophyll and proline content of four-year-old P. sargentii seedlings after 30 days of drought stress. In the trees subjected to drought stress treatment, soil moisture content decreased, and the fresh weight of the aboveground part of the plant decreased. However, there was no significant difference in the root growth of the dried plants. Among the photosynthesis parameters, Pn MAX, E and gs showed a significant (p  <  0.001) decrease after 15 days in dry-stressed seedlings, but there was no difference between treatments in WUE until 20 days, and there was a significant (p  <  0.001) difference after 24 days. Chlorophyll fluorescence parameters, Fv/Fm, ΦPSII, Rfd, NPQ, and Pn MAX, also increased after 10 days in dry-stressed seedlings, but these changes did not reach statistical significance compared to the control treatment. These results may suggest that drought stress highly correlates with photosynthesis and chlorophyll fluorescence parameters. Chlorophyll content also significantly decreased in the seedlings under drought stress compared with the control treatment. The proline content decreased until the 10th day of drought stress treatment and increased after the 15th day, showing an increase of 10.9% on the 15th day and 57.1% on the 30th day, compared to the control treatment. These results suggest that photosynthesis, chlorophyll fluorescence parameters, and proline content can be used to evaluate drought stress in trees. The results of this study can contribute to the management of forests, such as the irrigation of trees when pore control ability and photosynthesis ability decrease. creator: Eon Ju Jin creator: Jun-Hyuk Yoon creator: Hyeok Lee creator: Eun Ji Bae creator: Seong Hyeon Yong creator: Myung Suk Choi uri: https://doi.org/10.7717/peerj.15954 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Jin et al.