title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=379 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Glomeromycota associations with bamboos (Bambusoideae) worldwide, a qualitative systematic review of a promising symbiosis link: https://peerj.com/articles/16151 last-modified: 2023-11-09 description: BackgroundAround the world, bamboos are ecologically, economically, and culturally important plants, particularly in tropical regions of Asia, America, and Africa. The association of this plant group with arbuscular mycorrhizal fungi belonging to the phylum Glomeromycota is still a poorly studied field, which limits understanding of the reported ecological and physiological benefits for the plant, fungus, soil, and ecosystems under this symbiosis relationship.MethodsThrough a qualitative systematic review following the PRISMA framework for the collection, synthesis, and reporting of evidence, this paper presents a compilation of the research conducted on the biology and ecology of the symbiotic relationship between Glomeromycota and Bambusoideae from around the world. This review is based on academic databases enriched with documents retrieved using different online databases and the Google Scholar search engine.ResultsThe literature search yielded over 6,000 publications, from which 18 studies were included in the present review after a process of selection and validation. The information gathered from the publications included over 25 bamboo species and nine Glomeromycota genera from eight families, distributed across five countries on two continents.ConclusionThis review presents the current state of knowledge regarding the symbiosis between Glomeromycota and Bambusoideae, while reflecting on the challenges and scarcity of research on this promising association found across the world. creator: Juan José Sánchez-Matiz creator: Lucia Ana Díaz-Ariza uri: https://doi.org/10.7717/peerj.16151 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sánchez-Matiz and Díaz-Ariza title: Manipulating network connectance by altering plant attractiveness link: https://peerj.com/articles/16319 last-modified: 2023-11-09 description: BackgroundMutualistic interactions between plants and their pollinating insects are critical to the maintenance of biodiversity. However, we have yet to demonstrate that we are able to manage the structural properties of these networks for the purposes of pollinator conservation and preserving functional outcomes, such as pollination services. Our objective was to explore the extent of our ability to experimentally increase, decrease, and maintain connectance, a structural attribute that reflects patterns of insect visitation and foraging preferences. Patterns of connectance relate to the stability and function of ecological networks.MethodsWe implemented a 2-year field experiment across eight sites in urban Dublin, Ireland, applying four agrochemical treatments to fixed communities of seven flowering plant species in a randomized block design. We spent ~117 h collecting 1,908 flower-visiting insects of 92 species or morphospecies with standardized sampling methods across the 2 years. We hypothesized that the fertilizer treatment would increase, herbicide decrease, and a combination of both maintain the connectance of the network, relative to a control treatment of just water.ResultsOur results showed that we were able to successfully increase network connectance with a fertilizer treatment, and maintain network connectance with a combination of fertilizer and herbicide. However, we were not successful in decreasing network connectance with the herbicide treatment. The increase in connectance in the fertilized treatment was due to an increased species richness of visiting insects, rather than changes to their abundance. We also demonstrated that this change was due to an increase in the realized proportion of insect visitor species rather than increased visitation by common, generalist species of floral visitors. Overall, this work suggests that connectance is an attribute of network structure that can be manipulated, with implications for management goals or conservation efforts in these mutualistic communities. creator: Laura Russo creator: Jane C. Stout uri: https://doi.org/10.7717/peerj.16319 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Russo and Stout title: Impact analysis of moisture stress on growth and yield of cotton using DSSAT-CROPGRO-cotton model under semi-arid climate link: https://peerj.com/articles/16329 last-modified: 2023-11-09 description: Adequate soil moisture around the root zone of the crops is essential for optimal plant growth and productivity throughout the crop season, whereas excessive as well as deficient moisture is usually detrimental. A field experiment was conducted on cotton (Gossipium hirsuttum) with three water regimes (viz. well-watered (control); rainfed after one post-sowing irrigation (1-POSI) and rainfed after two post-sowing irrigations (2-POSI)) in main plots and application of eight osmoprotectants in sub plots of Split plot design to quantify the loss of seed cotton yield (SCY) under high and mild moisture stress. The DSSAT-CROPGRO-cotton model was calibrated to validate the response of cotton crop to water stress. Results elucidated that in comparison of well watered (control) crop, 1-POSI and 2-POSI reduced plant height by 13.5–28.4% and lower leaf area index (LAI) by 21.6–37.6%. Pooled analysis revealed that SCY under control was higher by 1,127 kg ha−1 over 1-POSI and 597 kg ha−1 than 2-POSI. The DSSAT-CROPGRO-cotton model fairly simulated the cotton yield as evidenced by good accuracy (d-stat ≥ 0.92) along with lower root mean square error (RMSE) of ≤183.2 kg ha−1; mean absolute percent error (MAPE) ≤6.5% under different irrigation levels. Similarly, simulated and observed biomass also exhibited good agreement with ≥0.98 d-stat; ≤533.7 kg ha−1 RMSE; and ≤4.6% MAPE. The model accurately simulated the periodical LAI, biomass and soil water dynamics as affected by varying water regimes in conformity with periodical observations. Both the experimental and the simulated results confirmed the decline of SCY with any degree of water stress. Thus, a well calibrated DSSAT-CROPGRO-cotton model may be successfully used for estimating the crop performance under varying hydro-climatic conditions. creator: Rotash Kumar creator: Sudhir Kumar Mishra creator: Kulvir Singh creator: Ibrahim Al-Ashkar creator: Muhammad Aamir Iqbal creator: Muhammad Noor Muzamil creator: Muhammad Habib ur Rahman creator: Ayman El Sabagh uri: https://doi.org/10.7717/peerj.16329 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kumar et al. title: A novel metabolism-related gene signature in patients with hepatocellular carcinoma link: https://peerj.com/articles/16335 last-modified: 2023-11-09 description: Hepatocellular carcinoma (HCC) remains a global challenge as it is the sixth most common neoplasm worldwide and the third leading cause of cancer-related death. A key feature of HCC is abnormal metabolism, which promotes cancer cell proliferation, survival, invasion, and metastasis. However, the significance of metabolism-related genes (MRGs) in HCC remains to be elucidated. Here, we aim to establish a novel metabolism-related prognostic signature for the prediction of patient outcomes and to investigate the value of MRG expression in the prognostic prediction of HCC. In our research, a Metabolism-Related Risk Score (MRRS) model was constructed using 14 MRGs (DLAT, SEPHS1, ACADS, UCK2, GOT2, ADH4, LDHA, ME1, TXNRD1, B4GALT2, AK2, PTDSS2, CSAD, and AMD1). The Kaplan-Meier curve confirmed that the MRRS has a high accuracy in predicting the prognosis of HCC patients (p < 0.001). According to the MRRS model, the area under the curve (AUC) values for predicting the prognosis of patients with hepatocellular carcinoma at 1, 3, and 5 years reached 0.829, 0.760, and 0.739, respectively. Functional analyses revealed that signaling pathways associated with the cell cycle were largely enriched by differential genes between high and low-risk groups. In addition, dendritic cells (DCs) (p < 0.001), CD4+ T cells (p < 0.01), CD8+ T cells (p < 0.001), B cells (p < 0.001), neutrophils (p < 0.001), macrophages (p < 0.001) had a higher proportion of infiltrates in high-risk populations. Low GOT2 expression is associated with poor prognosis in patients with hepatocellular carcinoma. Knockdown of GOT2 significantly increased the migration capacity of the Huh7 and MHCC97H hepatocellular carcinoma lines. Our research reveals that GOT2 is negatively related to the survival of patients with hepatocellular carcinoma and GOT2 may contribute to tumor progression by inhibiting the ability of tumor cells to migrate. creator: Bin Ru creator: Jiaqi Hu creator: Nannan Zhang creator: Quan Wan uri: https://doi.org/10.7717/peerj.16335 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Ru et al. title: Comparative study of the efficacy of intra-arterial and intravenous transplantation of human induced pluripotent stem cells-derived neural progenitor cells in experimental stroke link: https://peerj.com/articles/16358 last-modified: 2023-11-09 description: BackgroundCell therapy using neural progenitor cells (NPCs) is a promising approach for ischemic stroke treatment according to the results of multiple preclinical studies in animal stroke models. In the vast majority of conducted animal studies, the therapeutic efficacy of NPCs was estimated after intracerebral transplantation, while the information of the effectiveness of systemic administration is limited. Nowadays, several clinical trials aimed to estimate the safety and efficacy of NPCs transplantation in stroke patients were also conducted. In these studies, NPCs were transplanted intracerebrally in the subacute/chronic phase of stroke. The results of clinical trials confirmed the safety of the approach, however, the degree of functional improvement (the primary efficacy endpoint) was not sufficient in the majority of the studies. Therefore, more studies are needed in order to investigate the optimal transplantation parameters, especially the timing of cell transplantation after the stroke onset. This study aimed to evaluate the therapeutic effects of intra-arterial (IA) and intravenous (IV) administration of NPCs derived from induced pluripotent stem cells (iNPCs) in the acute phase of experimental stroke in rats. Induced pluripotent stem cells were chosen as the source of NPCs as this technology is perspective, has no ethical concerns and provides the access to personalized medicine.MethodsHuman iNPCs were transplanted IA or IV into male Wistar rats 24 h after the middle cerebral artery occlusion stroke modeling. Therapeutic efficacy was monitored for 14 days and evaluated in comparison with the cell transplantation-free control group. Additionally, cell distribution in the brain was assessed.ResultsThe obtained results show that both routes of systemic transplantation (IV and IA) significantly reduced the mortality and improved the neurological deficit of experimental animals compared to the control group. At the same time, according to the MRI data, only IA administration led to faster and prominent reduction of the stroke volume. After IA administration, iNPCs transiently trapped in the brain and were not detected on day 7 after the transplantation. In case of IV injection, transplanted cells were not visualized in the brain. The obtained data demonstrated that the systemic transplantation of human iNPCs in the acute phase of ischemic stroke can be a promising therapeutic strategy. creator: Elvira Cherkashova creator: Daria Namestnikova creator: Georgiy Leonov creator: Ilya Gubskiy creator: Kirill Sukhinich creator: Pavel Melnikov creator: Vladimir Chekhonin creator: Konstantin Yarygin creator: Dmitry Goldshtein creator: Diana Salikhova uri: https://doi.org/10.7717/peerj.16358 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Cherkashova et al. title: Bone marrow mesenchymal stem cell-derived exosomal microRNA regulates microglial polarization link: https://peerj.com/articles/16359 last-modified: 2023-11-09 description: ObjectiveThis study aimed to explore the effects of bone marrow mesenchymal stem cell (BMSC)-derived exosomal miR-146a-5p on microglial polarization and the potential underlying mechanisms in oxygen-glucose deprivation (OGD)-exposed microglial cells.MethodsExosomes were isolated from BMSCs, and their characteristics were examined. The effects of BMSC-derived exosomes on microglial polarization were investigated in OGD-exposed BV-2 cells. Differentially expressed miRNAs were identified and their biological function was explored using enrichment analyses. The regulatory role of miR-146a-5p in microglial polarization was studied via flow cytometry. Finally, the downstream target gene Traf6 was validated, and the role of the miR-146a-5p/Traf6 axis in modulating microglial polarization was investigated in OGD-exposed BV-2 cells.ResultsBMSC-derived exosomes were successfully isolated and characterized. A total of 10 upregulated and 33 downregulated miRNAs were identified. Exosomal treatment resulted in significant changes in microglial polarization markers. miR-146a-5p was found to be significantly downregulated in OGD-exposed microglial cells treated with exosomes. Manipulation of miR-146a-5p expression modulated microglial polarization. Moreover, the miR-146a-5p/Traf6 axis regulated microglial polarization.ConclusionOur findings demonstrate that BMSC-derived exosomal via miR-146a-5p modulates microglial polarization by targeting Traf6, providing a potential thermal target for the treatment of neurological diseases involving microglial activation. creator: Xianwei Huang creator: Xiong Liu creator: Jiaqi Zeng creator: Penghui Du creator: Xiaodong Huang creator: Jiyan Lin uri: https://doi.org/10.7717/peerj.16359 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huang et al. title: Confidence intervals for ratio of means of delta-lognormal distributions based on left-censored data with application to rainfall data in Thailand link: https://peerj.com/articles/16397 last-modified: 2023-11-09 description: Thailand is a country that is prone to both floods and droughts, and these natural disasters have significant impacts on the country’s people, economy, and environment. Estimating rainfall is an important part of flood and drought prevention. Rainfall data typically contains both zero and positive observations, and the distribution of rainfall often follows the delta-lognormal distribution. However, it is important to note that rainfall data can be censored, meaning that some values may be missing or truncated. The interval estimator for the ratio of means will be useful when comparing the means of two samples. The purpose of this article was to compare the performance of several approaches for statistically analyzing left-censored data. The performance of the confidence intervals was evaluated using the coverage probability and average length, which were assessed through Monte Carlo simulation. The approaches examined included several variations of the generalized confidence interval, the Bayesian, the parametric bootstrap, and the method of variance estimates recovery approaches. For (ξ1, ξ2) = (0.10,0.10), simulations showed that the Bayesian approach would be a suitable choice for constructing the credible interval for the ratio of means of delta-lognormal distributions based on left-censored data. For (ξ1, ξ2) = (0.10,0.25), the parametric bootstrap approach was a strong alternative for constructing the confidence interval. However, the generalized confidence interval approach can be considered to construct the confidence when the sample sizes are increase. Practical applications demonstrating the use of these techniques on rainfall data showed that the confidence interval based on the generalized confidence interval approach covered the ratio of population means and had the smallest length. The proposed approaches’ effectiveness was illustrated using daily rainfall datasets from the provinces of Chiang Rai and Chiang Mai in Thailand. creator: Warisa Thangjai creator: Sa-Aat Niwitpong uri: https://doi.org/10.7717/peerj.16397 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Thangjai and Niwitpong title: Investigating altered brain functional hubs and causal connectivity in coronary artery disease with cognitive impairment link: https://peerj.com/articles/16408 last-modified: 2023-11-09 description: BackgroundCoronary artery disease (CAD) and cognitive impairment (CI) have become significant global disease and medical burdens. There have been several reports documenting the alterations in regional brain function and their correlation with CI in CAD patients. However, there is limited research on the changes in brain network connectivity in CAD patients. To investigate the resting-state connectivity and further understand the effective connectivity strength and directionality in patients with CAD, we utilized degree centrality (DC) and spectral dynamic causal modeling (spDCM) to detect functional hubs in the whole brain network, followed by an analysis of directional connections. Using the aforementioned approaches, it is possible to investigate the hub regions and aberrant connections underlying the altered brain function in CAD patients, providing neuroimaging evidence for the cognitive decline in patients with coronary artery disease.Materials and MethodsThis study was prospectively conducted involving 24 patients diagnosed with CAD and 24 healthy controls (HC) who were matched in terms of age, gender, and education. Functional MRI (fMRI) scans were utilized to investigate brain activity in these individuals. Neuropsychological examinations were performed on all participants. DC analysis and spDCM were employed to investigate abnormal brain networks in patients with CAD. Additionally, the association between effective connectivity strength and cognitive function in patients with CAD was examined based on the aforementioned results.ResultsBy assessing cognitive functions, we discovered that patients with CAD exhibited notably lower cognitive function compared to the HC group. By utilizing DC analysis and spDCM, we observed significant reductions in DC values within the left parahippocampal cortex (PHC) and the left medial temporal gyrus (MTG) in CAD patients when compared to the control group. In terms of effective connectivity, we observed the absence of positive connectivity between the right superior frontal gyrus (SFG) and PHC in CAD patients. Moreover, there was an increase in negative connectivity from PHC and MTG to SFG, along with a decrease in the strength of positive connectivity between PHC and MTG. Furthermore, we identified a noteworthy positive correlation (r = 0.491, p = 0.015) between the strength of connectivity between the PHC and the MTG and cognitive function in CAD patients.ConclusionsThese research findings suggest that alterations in the connectivity of the brain networks involving SFG, PHC, and MTG in CAD patients may mediate changes in cognitive function. creator: Rui Qin creator: Tong Li creator: Cuicui Li creator: Lin Li creator: Ximing Wang creator: Li Wang uri: https://doi.org/10.7717/peerj.16408 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Qin et al. title: Arbuscular mycorrhizal fungi alter rhizosphere fungal community characteristics of Acorus calamus to improve Cr resistance link: https://peerj.com/articles/15681 last-modified: 2023-11-08 description: To investigate changes in fungal community characteristics under different Cr(VI) concentration stresses and the advantages of adding arbuscular mycorrhizal fungi (AMF), we used high throughput sequencing to characterize the fungal communities. Cr(VI) stress reduced rhizosphere soil SOM (soil organic matter) content and AMF addition improved this stress phenomenon. There were significant differences in fungal community changes under different Cr(VI) concentrations. The fungal community characteristics changed through inhibition of fungal metabolic ability, as fungal abundance increased after AMF addition, and the fungal diversity increased under high Cr(VI) concentration. The dominant phyla were members of the Ascomycota, Basidiomycota, Mortierellomycota, and Rozellomycota. Dominant groups relevant to Cr resistance were Ascomycota and Basidiomycota fungi. Moreover, Fungal community characteristics were analyzed using high-throughput sequencing of the cytochrome c metabolic pathway, NADH dehydrogenase, and NADH: ubiquinone reductase and all these functions were enhanced after AMF addition. Therefore, Cr(VI) stress significantly affects fungal community structure, while AMF addition could increase its SOM content, and metabolic capacity, and improve fungal community tolerance to Cr stress. This study contributed to the understanding response of rhizosphere fungal community in AMF-assisted wetland phytoremediation under Cr stress. creator: Guodong Xia creator: Sixi Zhu creator: Wei Zhao creator: Xiuqing Yang creator: Luying Sheng creator: Huan Mao uri: https://doi.org/10.7717/peerj.15681 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xia et al. title: AL360181.1 promotes proliferation and invasion in colon cancer and is one of ten m6A-related lncRNAs that predict overall survival link: https://peerj.com/articles/16123 last-modified: 2023-11-08 description: BackgroundN6-methyladenosine (m6A) exerted a pivotal role in colon cancer. Nevertheless, the long non-coding RNAs (lncRNAs) associated with this process have yet to be elucidated.MethodsThe open-access data used for analysis was downloaded from The Cancer Genome Atlas (TCGA) database for analysis, employing the R software for computational evaluations. The RNA level of specific molecules was assessed using the quantitative real-time PCR. CCK8, colony formation and transwell assay were used to evaluate the proliferation, invasion and migration ability of colon cancer cells.ResultsHere, we identified the m6A regulators from TCGA data and subsequently pinpointed lncRNAs with a —Cor— > 0.3 and P < 0.05, categorizing them as m6A-associated lncRNAs. Moreover, we formulated a prognosis signature rooted in ten m6A-related lncRNAs, consisting of AL360181.1, PCAT6, SNHG26, AC016876.1, AC104667.2, AL114730.3, LINC02257, AC147067.1, AP006621.3 and AC009237.14. This signature exhibited notable predictive accuracy in gauging patient survival. Immune-related evaluations revealed varied immune cell infiltration patterns across different risk groups, with our findings suggesting superior immunotherapy response in low-risk patients. Biological enrichment analysis indicated that the high-risk patients had a higher activity of multiple carcinogenic pathways, including glycolysis. The previously unreported lncRNA, AL360181.1, displayed a connection to glycolytic activity and diminished survival rates, warranting further investigation. The result indicated that AL360181.1 was correlated with more aggressive clinical characteristics. Immune infiltration assessments found AL360181.1 to have a positive correlation with Tcm infiltration, but an inverse relationship with entities like Th2 cells, T cells, neutrophils and macrophages. Biological enrichment analysis indicated that the pathways of WNT/β-catenin, pancreas beta cells, hedgehog signaling and some metabolism pathways were upregulated in high AL360181.1 patients. In vitro experiments showed that AL360181.1 was upregulated in the colon cancer cells. Moreover, AL360181.1 significantly promotes the proliferation, invasion and migration of colon cancer cells.ConclusionsOur results can provide direction for future studies on m6A-related lncRNA in colon cancer. creator: Yi Luo creator: Yayun Xie creator: Dejun Wu creator: Bingyi Wang creator: Helei Lu creator: Zhiqiang Wang creator: Yingjun Quan creator: Bo Han uri: https://doi.org/10.7717/peerj.16123 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Luo et al.