title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=544 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Epigenetic regulation of dental-derived stem cells and their application in pulp and periodontal regeneration link: https://peerj.com/articles/14550 last-modified: 2023-01-03 description: Dental-derived stem cells have excellent proliferation ability and multi-directional differentiation potential, making them an important research target in tissue engineering. An increasing number of dental-derived stem cells have been discovered recently, including dental pulp stem cells (DPSCs), stem cells from exfoliated deciduous teeth (SHEDs), stem cells from apical papilla (SCAPs), dental follicle precursor cells (DFPCs), and periodontal ligament stem cells (PDLSCs). These stem cells have significant application prospects in tissue regeneration because they are found in an abundance of sources, and they have good biocompatibility and are highly effective. The biological functions of dental-derived stem cells are regulated in many ways. Epigenetic regulation means changing the expression level and function of a gene without changing its sequence. Epigenetic regulation is involved in many biological processes, such as embryonic development, bone homeostasis, and the fate of stem cells. Existing studies have shown that dental-derived stem cells are also regulated by epigenetic modifications. Pulp and periodontal regeneration refers to the practice of replacing damaged pulp and periodontal tissue and restoring the tissue structure and function under normal physiological conditions. This treatment has better therapeutic effects than traditional treatments. This article reviews the recent research on the mechanism of epigenetic regulation of dental-derived stem cells, and the core issues surrounding the practical application and future use of pulp and periodontal regeneration. creator: Yuyang Chen creator: Xiayi Wang creator: Zhuoxuan Wu creator: Shiyu Jia creator: Mian Wan uri: https://doi.org/10.7717/peerj.14550 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: Agricultural water allocation with climate change based on gray wolf optimization in a semi-arid region of China link: https://peerj.com/articles/14577 last-modified: 2023-01-03 description: BackgroundWe quantified and evaluated the allocation of soil and water resources in the Aksu River Basin to measure the consequences of climate change on an agricultural irrigation system.MethodsWe first simulated future climate scenarios in the Aksu River Basin by using a statistical downscaling model (SDSM). We then formulated the optimal allocation scheme of agricultural water as a multiobjective optimization problem and obtained the Pareto optimal solution using the multi-objective grey wolf optimizer (MOGWO). Finally, optimal allocations of water and land resources in the basin at different times were obtained using an analytic hierarchy process (AHP).Results(1) The SDSM is able to simulate future climate change scenarios in the Aksu River Basin. Evapotranspiration (ET0) will increase significantly with variation as will the amount of available water albeit slightly. (2) To alleviate water pressure, the area of cropland should be reduced by 127.5 km2 under RCP4.5 and 377.2 km2 under RCP8.5 scenarios. (3) To be sustainable, the allocation ratio of forest land and water body should increase to 39% of the total water resource in the Aksu River Basin by 2050. creator: Zhidong Wang creator: Xining Zhao creator: Jinglei Wang creator: Ni Song creator: Qisheng Han uri: https://doi.org/10.7717/peerj.14577 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: Two new temporary ectoparasitic isopods (Cymothoida: Cymothooidea) from Korean waters with a note on geographical distributions of Rocinela Leach, 1818 and Gnathia Leach, 1814 link: https://peerj.com/articles/14593 last-modified: 2023-01-03 description: Two new species of temporary ectoparasitic isopods, Rocinela excavatasp. nov. and Gnathia obtusispinasp. nov., are reported from the southern Islands of the Korean Peninsula. Rocinela excavatasp. nov. is distinguishable from its related species by the following characteristics: (1) laterally stepped rostrum; (2) separated eyes; (3) propodal blade having eight robust setae; and (4) merus having four or five blunt robust setae in pereopods 1–3. Gnathia obtusispinasp. nov. differs from its congeners by the combination of the following characteristics: (1) body covered with numerous tubercles and setae, (2) cephalon having tooth-like paraocular ornamentations; and (3) frontal border having two inferior frontolateral processes. These two new species are the 13thRocinela species and 19thGnathia species in the temperate Northern Pacific region, respectively. Discovery of these new species represents high species diversity of the genera Rocinela Leach, 1818 and Gnathia Leach, 1814 worldwide as well as in the Northern Pacific region. In addition, faunal diversity analysis on the members of both genera revealed that Rocinela species show high-latitude diversity whereas Gnathia species have low-latitude diversity. creator: Sung Hoon Kim creator: Jong Guk Kim creator: Seong Myeong Yoon uri: https://doi.org/10.7717/peerj.14593 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kim et al. title: Integrative genomic and transcriptomic analyses of a bud sport mutant ‘Jinzao Wuhe’ with the phenotype of large berries in grapevines link: https://peerj.com/articles/14617 last-modified: 2023-01-03 description: BackgroundBud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. ‘Jinzao Wuhe’ is a bud sport of the elite cultivar ‘Himord Seedless’ with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear.MethodsWhole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for ‘Jinzao Wuhe’ and its maternal plant ‘Himord Seedless’ were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation.ResultsIn two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between ‘Himord Seedless’ and ‘Jinzao Wuhe’ harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine.ConclusionOur results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars. creator: Jianquan Huang creator: Guan Zhang creator: Yanhao Li creator: Mingjie Lyu creator: He Zhang creator: Na Zhang creator: Rui Chen uri: https://doi.org/10.7717/peerj.14617 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Huang et al. title: Evolutionary analysis of endogenous intronic retroviruses in primates reveals an enrichment in transcription binding sites associated with key regulatory processes link: https://peerj.com/articles/14431 last-modified: 2022-12-22 description: BackgroundEndogenous retroviruses (ERVs) are the result of the integration of retroviruses into host DNA following germline infection. Endogenous retroviruses are made up of three main genes: gag, pol, and env, each of which encodes viral proteins that can be conserved or not. ERVs have been observed in a wide range of vertebrate genomes and their functions are associated with viral silencing and gene regulation.ResultsIn this work, we studied the evolutionary history of endogenous retroviruses associated with five human genes (INPP5B, DET1, PSMA1, USH2A, and MACROD2), which are located within intron sections. To verify the retroviral origin of the candidates, several approaches were used to detect and locate ERV elements. Both orthologous and paralogous genes were identified by Ensembl and then analyzed for ERV presence using RetroTector. A phylogenetic tree was reconstructed to identify the minimum time point of ERV acquisition. From that search, we detected ERVs throughout the primate lineage and in some other groups. Also, we identified the minimum origin of the ERVs from the parvorder Catarrhini to the Homininae subfamily.ConclusionsWith the data collected, and by observing the transcription factors annotated inside ERVs, we propose that these elements play a relevant role in gene expression regulation and they probably possess important features for tumorigenesis control. creator: Melissa Calero-Layana creator: Carmen López-Cruz creator: Agustín Ocaña creator: Eduardo Tejera creator: Vinicio Armijos-Jaramillo uri: https://doi.org/10.7717/peerj.14431 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Calero-Layana et al. title: Left ventricle dysfunction in patients with critical neonatal pulmonary stenosis: echocardiographic predictors. A single-center retrospective study link: https://peerj.com/articles/14056 last-modified: 2022-12-21 description: BackgroundThe aim of this study is to identify echocardiographic predictors of transient left ventricle dysfunction after pulmonary valve balloon dilatation (PVBD), in neonates with pulmonary valve stenosis (PVS) and atresia with intact septum (PAIVS) at birth.MethodsThe study includes patients admitted at the Bambino Gesù Children Hospital from January 2012 to January 2017. Clinical, echocardiographic and cardiac catheterization data before and after PVBD were retrospectively analyzed.ResultsTwenty-nine infants were included in the study (21 male and eight female). The median age was 5.8 ± 7.1 days. Eight patients developed transient LV dysfunction (three PAIVS and five PVS) and comparing data before and after the procedure, there was no difference in right ventricle geometrical and functional parameters except for evidence of at least moderate pulmonary valve regurgitation after PVBD.ConclusionModerate to severe degree pulmonary valve regurgitation was significant associated to LV dysfunction (p < 0.05) in PVS and PAIVS patients. creator: Carolina D’Anna creator: Alessio Franceschini creator: Micol Rebonato creator: Paolo Ciliberti creator: Claudia Esposito creator: Roberto Formigari creator: Maria Giulia Gagliardi creator: Paolo Guccione creator: Gianfranco Butera creator: Lorenzo Galletti creator: Marcello Chinali uri: https://doi.org/10.7717/peerj.14056 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 D’Anna et al. title: Modeling the response of Japanese quail to arginine intake link: https://peerj.com/articles/14337 last-modified: 2022-12-21 description: BackgroundUnderstanding how Japanese quails respond to arginine intake has been an objective that previous studies have not fulfilled. The main responses to be quantified include the arginine requirement for maintenance (mg/kg0.67) and egg mass production (mg/g). Quantifying maintenance and production relationships are essential steps for predicting animal response. The current study aimed to describe how quails respond to arginine intake and determine arginine requirements for maintenance and egg production in Japanese quails.MethodsThe experiment was carried out in a completely randomized design, with seven treatments and seven replicates with individual birds as experimental units. The arginine levels were: 2.43, 3.64, 4.85, 6.07, 9.07, 12.13, and 14.56 g/kg. The experiment lasted for eight weeks. The variables analyzed were daily arginine intake, daily arginine deposition in eggs, and body weight. The data were analyzed using a mixed model, with the experimental unit being the random effect and the experimental levels of arginine as a fixed effect. When the effect of arginine levels was detected (P ≤ 0.05), saturation kinetics and an exponential model with four parameters (monomolecular) were adopted. ANOVA results indicated that dietary arginine levels significantly affected (P < 0.01) the analyzed variables. The formulation strategy of the experimental diets allowed amplitude in the dietary arginine levels, and according to bird responses, arginine was the limiting nutrient.ResultsThe arginine requirement for body weight maintenance (BW0.67) was estimated to be 90 mg/kg BW0.67 by the monomolecular function. The requirement for egg mass (EM) production was estimated to be 25 mg/g per egg. A factorial model was parameterized as follows: daily arginine intake mg/bird = 90 × BW0.67 + 25 × EM ± 12 mg. The model was applied to data obtained from literature, and the resultant error was within the expected limit of 12 mg. The recommended daily arginine intake for the daily production of 11 g of egg and 180 g of BW was determined to be 304 mg/bird. The current study provides procedures that researchers can easily adopt. creator: Manoela Sousa creator: Michele Lima creator: Rita Brito Vieira creator: Jaqueline Pavanini creator: Nelson José Peruzzi creator: Erikson Raimundo creator: Daniel Santos creator: Edney Silva uri: https://doi.org/10.7717/peerj.14337 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Sousa et al. title: A new Meckel’s cartilage from the Devonian Hangenberg black shale in Morocco and its position in chondrichthyan jaw morphospace link: https://peerj.com/articles/14418 last-modified: 2022-12-21 description: Fossil chondrichthyan remains are mostly known from their teeth, scales or fin spines only, whereas their cartilaginous endoskeletons require exceptional preservational conditions to become fossilized. While most cartilaginous remains of Famennian (Late Devonian) chondrichthyans were found in older layers of the eastern Anti-Atlas, such fossils were unknown from the Hangenberg black shale (HBS) and only a few chondrichthyan teeth had been found therein previously. Here, we describe a Meckel’s cartilage from the Hangenberg black shale in Morocco, which is the first fossil cartilage from these strata. Since no teeth or other skeletal elements have been found in articulation, we used elliptical Fourier (EFA), principal component (PCA), and hierarchical cluster (HCA) analyses to morphologically compare it with 41 chondrichthyan taxa of different size and age and to evaluate its possible systematic affiliation. PCA and HCA position the new specimen closest to some acanthodian and elasmobranch jaws. Accordingly, a holocephalan origin was excluded. The jaw shape as well as the presence of a polygonal pattern, typical for tessellated calcified cartilage, suggest a ctenacanth origin and we assigned the new HBS Meckel’s cartilage to the order Ctenacanthiformes with reservations. creator: Merle Greif creator: Humberto G. Ferrón creator: Christian Klug uri: https://doi.org/10.7717/peerj.14418 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Greif et al. title: Future stem cell analysis: progress and challenges towards state-of-the art approaches in automated cells analysis link: https://peerj.com/articles/14513 last-modified: 2022-12-21 description: Background and AimsA microscopic image has been used in cell analysis for cell type identification and classification, cell counting and cell size measurement. Most previous research works are tedious, including detailed understanding and time-consuming. The scientists and researchers are seeking modern and automatic cell analysis approaches in line with the current in-demand technology.ObjectivesThis article provides a brief overview of a general cell and specific stem cell analysis approaches from the history of cell discovery up to the state-of-the-art approaches.MethodologyA content description of the literature study has been surveyed from specific manuscript databases using three review methods: manuscript identification, screening, and inclusion. This review methodology is based on Prism guidelines in searching for originality and novelty in studies concerning cell analysis.ResultsBy analysing generic cell and specific stem cell analysis approaches, current technology offers tremendous potential in assisting medical experts in performing cell analysis using a method that is less laborious, cost-effective, and reduces error rates.ConclusionThis review uncovers potential research gaps concerning generic cell and specific stem cell analysis. Thus, it could be a reference for developing automated cells analysis approaches using current technology such as artificial intelligence and deep learning. creator: Nurul Syahira Mohamad Zamani creator: Wan Mimi Diyana Wan Zaki creator: Zariyantey Abd Hamid creator: Aqilah Baseri Huddin uri: https://doi.org/10.7717/peerj.14513 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Mohamad Zamani et al. title: OPA1 supports mitochondrial dynamics and immune evasion to CD8+ T cell in lung adenocarcinoma link: https://peerj.com/articles/14543 last-modified: 2022-12-21 description: BackgroundMitochondrial fusion and fission were identified to play key roles during multiple biology process. Thus, we aim to investigate the roles of OPA1 in mitochondria fusion and immune evasion of non-small cell lung cancer cells.MethodsThe transcriptional activation of genes related to mitochondrial dynamics was determined by using multi-omics data in lung adenocarcinoma (LUAD). We elucidated the molecular mechanism and roles of OPA1 promoting lung cancer through single-cell sequencing and molecular biological experiments.ResultsHere, we found that copy number amplification of OPA1 and MFN1 were co-occurring and synergistically activated in tumor epithelial cells in lung cancer tissues. Both of OPA1 and MFN1 were highly expressed in LUAD tumor tissues and OPA1 high expression was associated with poor prognosis. In terms of mechanism, the damaged mitochondria activated the apoptotic signaling pathways, inducing cell cycle arrest and cell apoptosis. More interestingly, OPA1 deficiency damaged mitochondrial dynamics and further blocked the respiratory function to increase the sensitivity of tumor epithelial to CD8+ T cells in non-small cell lung cancer.ConclusionsOur study demonstrated the high co-occurrence of copy number amplification and co-expression of OPA1 and MFN1 in LUAD tissue, and further revealed the contribution of OPA1 in maintaining the mitochondria respiratory function and the ability of immune evasion to CD8+ T cells of LUAD. creator: Ying Wang creator: Yadong Li creator: Xuanwei Jiang creator: Yayun Gu creator: Hui Zheng creator: Xiaoxuan Wang creator: Haotian Zhang creator: Jixiang Wu creator: Yang Cheng uri: https://doi.org/10.7717/peerj.14543 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Wang et al.