title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=503 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Triptoquinone A and B exercise a therapeutic effect in systemic lupus erythematosus by regulating NLRC3 link: https://peerj.com/articles/15395 last-modified: 2023-06-09 description: The autoimmune disorder systemic lupus erythematosus (SLE) is multifaceted, with limited therapeutic alternatives and detrimental side effects, particularly on bones and joints. This research endeavors to examine the curative potential and underlying mechanisms of in addressing SLE-associated bone and joint complications. Triptoquinone A and triptoquinone B, constituents of Tripterygium wilfordii polyglycoside tablets (TGTs), exhibit antioxidant and anti-inflammatory attributes; nonetheless, its function in SLE therapy remains elusive. This investigation delves into the role of oxidative stress in systemic lupus erythematosus (SLE) and probes the prospective remedial effects of triptoquinone A and triptoquinone B on inflammation and cartilage deterioration in SLE-affected joints. Employing bioinformatics analyses, differentially expressed genes (DEGs) and protein-protein interactions were discerned in SLE, rheumatoid arthritis (RA), and osteoarthritis (OA) datasets. Enrichment analyses unveiled shared genes implicated in immune system regulation and toll-like receptor signaling pathways, among others. Subsequent examination of triptoquinone A and triptoquinone B revealed their capacity to diminish NLRC3 expression in chondrocytes, resulting in decreased pro-inflammatory cytokine levels and cartilage degradation enzyme expression. Suppression of NLRC3 augmented the protective effects of triptoquinone A and B, implying that targeting NLRC3 may constitute a potential therapeutic strategy for inflammation and cartilage degeneration-associated conditions in SLE patients. Our discoveries indicate that triptoquinone A and triptoquinone B may impede SLE progression via the NLRC3 axis, offering potential benefits for SLE-affected bone and joint health. creator: Qinyao Xu creator: Xiangzhi Zhang creator: Shangqing Ge creator: Chang Xu creator: Yuanfan Lv creator: Zongwen Shuai uri: https://doi.org/10.7717/peerj.15395 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Xu et al. title: Reliability and validity of the Körperkoordinationstest Für Kinder in Chinese children link: https://peerj.com/articles/15447 last-modified: 2023-06-09 description: BackgroundThe Körperkoordinationstest Für Kinder (KTK) is a reliable and low-cost motor coordination test tool that has been used in several countries. However, whether the KTK is a reliable and valid instrument for use in Chinese children has not been assessed. Additionally, because the KTK was designed to incorporate locomotor, object control, and stability skills, and there is a lack of measurement tools that include stability skills assessment for Chinese children, the KTK’s value and validity are worth discussing.MethodsA total of 249 primary school children (131 boys; 118 girls) aged 9–10 years from Shanghai were recruited in this study. Against the Test of Gross Motor Development-3 (TGMD-3), the concurrent validity of the KTK was assessed. We also tested the retest reliability and internal consistency of the KTK.ResultsThe test–retest reliability of the KTK was excellent (overall: r = 0.951; balancing backwards: r = 0.869; hopping for height: r = 0.918; jumping sideways: r = 0.877; moving sideways: r = 0.647). Except for the boys, the internal consistency of the KTK was higher than the acceptable level of Cronbach’s α > 0.60 (overall: α = 0.618; boys: α = 0.583; girls: α = 0.664). Acceptable concurrent validity was found between the total scores for the KTK and TGMD-3 (overall: r = 0.420, p < 0.001; boys: r = 0.411, p < 0.001; girls: r = 0.437, p < 0.001).DiscussionThe KTK is a reliable instrument for assessing the motor coordination of children in China. As such, the KTK can be used to monitor the level of motor coordination in Chinese children. creator: Kai Li creator: Ran Bao creator: Hyunshik Kim creator: Jiameng Ma creator: Ci Song creator: Sitong Chen creator: Yujun Cai uri: https://doi.org/10.7717/peerj.15447 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li et al. title: Allopatric speciation is more prevalent than parapatric ecological divergence in a recent high-Andean diversification (Linochilus: Asteraceae) link: https://peerj.com/articles/15479 last-modified: 2023-06-09 description: Elucidating how species accumulate in diversity hotspots is an ongoing debate in evolutionary biology. The páramo, in the Northern Andes, has remarkably high indices of plant diversity, endemicity, and diversification rates. A hypothesis for explaining such indices is that allopatric speciation is high in the páramo given its island-like distribution. An alternative hypothesis is that the altitudinal gradient of the Andean topography provides a variety of niches that drive vertical parapatric ecological speciation. A formal test for evaluating the relative roles of allopatric and parapatric ecological speciation is lacking. The main aim of our study is to test which kind of speciation is more common in an endemic páramo genus. We developed a framework incorporating phylogenetics, species’ distributions, and a morpho-ecological trait (leaf area) to compare sister species and infer whether allopatric or parapatric ecological divergence caused their speciation. We applied our framework to the species-rich genus Linochilus (63 spp.) and found that the majority of recent speciation events in it (12 events, 80%) have been driven by allopatric speciation, while a smaller fraction (one event, 6.7%) is attributed to parapatric ecological speciation; two pairs of sister species produced inconclusive results (13.3%). We conclude that páramo autochthonous (in-situ) diversification has been primarily driven by allopatric speciation. creator: Oscar M. Vargas creator: Santiago Madriñán creator: Beryl Simpson uri: https://doi.org/10.7717/peerj.15479 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Vargas et al. title: Phenotypic and genetic diversity of doubled haploid bread wheat population and molecular validation for spike characteristics, end-use quality, and biofortification capacity link: https://peerj.com/articles/15485 last-modified: 2023-06-09 description: Increasing grain quality and nutritional value along with yield in bread wheat is one of the leading breeding goals. Selection of genotypes with desired traits using traditional breeding selection methods is very time-consuming and often not possible due to the interaction of environmental factors. By identifying DNA markers that can be used to identify genotypes with desired alleles, high-quality and bio-fortified bread wheat production can be achieved in a short time and cost-effectively. In the present study, 134 doubled haploid (DH) wheat lines and their four parents were phenotypically evaluated for yield components (spike characteristics), quality parameters, and grain Fe and Zn concentrations in two successive growing seasons. At the same time, ten genic simple sequence repeats (SSR) markers linked to genes related to the traits examined were validated and subsequently used for molecular characterization of trait-specific candidate genotypes. Significant genotypic variations were determined for all studied traits and many genotypes with desired phenotypic values were detected. The evaluation performed with 10 SSR markers revealed significant polymorphism between genotypes. The polymorphic information content (PIC) values of 10 markers ranged from 0.00 to 0.87. Six out of 10 SSRs could be more effective in representing the genotypic differentiation of the DH population as they demonstrated the highest genetic diversity. Both Unweighted Pair Group Method with Arithmetic Mean (UPGMA) clustering and STRUCTURE analyses divided 138 wheat genotypes into five (K = 5) main groups. These analyzes were indicative of genetic variation due to hybridization and segregation in the DH population and the differentiation of the genotypes from their parents. Single marker regression analysis showed that both Xbarc61 and Xbarc146 had significant relationships with grain Fe and Zn concentrations, while Xbarc61 related to spike characteristics and Xbarc146 related to quality traits, separately. Other than these, Xgwm282 was associated with spike harvest index, SDS sedimentation value and Fe grain concentration, while Gwm445 was associated with spikelet number, grain number per spike and grain Fe concentration. These markers were validated for the studied DH population during the present study and they could be effectively used for marker-assisted selection to improve grain yield, quality, and bio-fortification capacity of bread wheat. creator: Imren Kutlu creator: Sadettin Çelik creator: Yaşar Karaduman creator: Özcan Yorgancılar uri: https://doi.org/10.7717/peerj.15485 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Kutlu et al. title: Honey bees and bumble bees occupying the same landscape have distinct gut microbiomes and amplicon sequence variant-level responses to infections link: https://peerj.com/articles/15501 last-modified: 2023-06-09 description: The gut microbiome of bees is vital for the health of their hosts. Given the ecosystem functions performed by bees, and the declines faced by many species, it is important to improve our understanding of the amount of natural variation in the gut microbiome, the level of sharing of bacteria among co-occurring species (including between native and non-native species), and how gut communities respond to infections. We conducted 16S rRNA metabarcoding to discern the level of microbiome similarity between honey bees (Apis mellifera, N = 49) and bumble bees (Bombus spp., N = 66) in a suburban-rural landscape. We identified a total of 233 amplicon sequence variants (ASVs) and found simple gut microbiomes dominated by bacterial taxa belonging to Gilliamella, Snodgrassella, and Lactobacillus. The average number of ASVs per species ranged from 4.00–15.00 (8.79 ± 3.84, mean ± SD). Amplicon sequence variant of one bacterial species, G. apicola (ASV 1), was widely shared across honey bees and bumble bees. However, we detected another ASV of G. apicola that was either exclusive to honey bees, or represented an intra-genomic 16S rRNA haplotype variant in honey bees. Other than ASV 1, honey bees and bumble bees rarely share gut bacteria, even ones likely derived from outside environments (e.g., Rhizobium spp., Fructobacillus spp.). Honey bee bacterial microbiomes exhibited higher alpha diversity but lower beta and gamma diversities than those of bumble bees, likely a result of the former possessing larger, perennial hives. Finally, we identified pathogenic or symbiotic bacteria (G. apicola, Acinetobacter sp. and Pluralibacter sp.) that associate with Trypanosome and/or Vairimorpha infections in bees. Such insights help to determine bees’ susceptibility to infections should gut microbiomes become disrupted by chemical pollutants and contribute to our understanding of what constitutes a state of dysbiosis. creator: Navolle Amiri creator: Mia M. Keady creator: Haw Chuan Lim uri: https://doi.org/10.7717/peerj.15501 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Amiri et al. title: Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification link: https://peerj.com/articles/15117 last-modified: 2023-06-08 description: The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10–11 Ma. Today, there is only one permanent connection between the Orinoco and Negro (Amazon) basins, known as the Casiquiare Canal. However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (Paracheirodon axelrodi), the most important fish in the ornamental world market, is distributed in both basins. Here we investigated P. axelrodi phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and eight microsatellite loci were analyzed. As a result, we found two major genetic clusters as the most likely scenario (K = 2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and São Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K = 3 − 6), showing three major geographic clusters: Orinoco, Cucui, and the remaining Negro basin. Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance. creator: Diana Sanchez-Bernal creator: José Gregorio Martinez creator: Izeni Pires Farias creator: Tomas Hrbek creator: Susana Caballero uri: https://doi.org/10.7717/peerj.15117 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Sanchez-Bernal et al. title: Research progress on the bulb expansion and starch enrichment in taro (Colocasia esculenta (L). Schott) link: https://peerj.com/articles/15400 last-modified: 2023-06-08 description: BackgroundTaro is an important potato crop, which can be used as food, vegetable, feed, and industrial raw material. The yield and quality of taro are primarily determined by the expansion degree of taro bulb and the filling condition of starch, whereas the expansion of taro bulb is a complex biological process. However, little information is reviewed on the research progress of bulb expansion and starch enrichment in taro.MethodologyPubMed, Web of Science, and the China National Knowledge Infrastructure databases were searched for relevant articles. After removing duplicate articles and articles with little relevance, 73 articles were selected for review.ResultsThis article introduces the formation and development of taro bulb for workers engaged in taro research. The content includes the process of amyloplast formation at the cytological level and changes in bulb expansion and starch enrichment at physiological levels, which involve endogenous hormones and key enzyme genes for starch synthesis. The effects of environment and cultivation methods on taro bulb expansion were also reviewed.ConclusionsFuture research directions and research focus about the development of taro bulb were proposed. Limited research has been conducted on the physiological mechanism and hormone regulatory pathway of taro growth and development, taro bulb expansion, key gene expression, and starch enrichment. Therefore, the abovementioned research will become the key research direction in the future. creator: Erjin Zhang creator: Wenyuan Shen creator: Weijie Jiang creator: Wenlong Li creator: Xiaping Wan creator: Xurun Yu creator: Fei Xiong uri: https://doi.org/10.7717/peerj.15400 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Zhang et al. title: Inflammatory auxo-action in the stem cell division theory of cancer link: https://peerj.com/articles/15444 last-modified: 2023-06-08 description: Acute inflammation is a beneficial response to the changes caused by pathogens or injuries that can eliminate the source of damage and restore homeostasis in damaged tissues. However, chronic inflammation causes malignant transformation and carcinogenic effects of cells through continuous exposure to pro-inflammatory cytokines and activation of inflammatory signaling pathways. According to the theory of stem cell division, the essential properties of stem cells, including long life span and self-renewal, make them vulnerable to accumulating genetic changes that can lead to cancer. Inflammation drives quiescent stem cells to enter the cell cycle and perform tissue repair functions. However, as cancer likely originates from DNA mutations that accumulate over time via normal stem cell division, inflammation may promote cancer development, even before the stem cells become cancerous. Numerous studies have reported that the mechanisms of inflammation in cancer formation and metastasis are diverse and complex; however, few studies have reviewed how inflammation affects cancer formation from the stem cell source. Based on the stem cell division theory of cancer, this review summarizes how inflammation affects normal stem cells, cancer stem cells, and cancer cells. We conclude that chronic inflammation leads to persistent stem cells activation, which can accumulate DNA damage and ultimately promote cancer. Additionally, inflammation not only facilitates the progression of stem cells into cancer cells, but also plays a positive role in cancer metastasis. creator: Yi Luo creator: Jian-Hui Xiao uri: https://doi.org/10.7717/peerj.15444 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Luo and Xiao title: In vitro and in silico evaluation of the design of nano-phyto-drug candidate for oral use against Staphylococcus aureus link: https://peerj.com/articles/15523 last-modified: 2023-06-08 description: Onopordum acanthium is a medicinal plant with many important properties, such as antibacterial, anticancer, and anti-hypotensive properties. Although various studies reported the biological activities of O. acanthium, there is no study on its nano-phyto-drug formulation. The aim of this study is to develop a candidate nano-drug based on phytotherapeutic constituents and evaluate its efficiency in vitro and in silico. In this context, poly (lactic-co-glycolic acid) (PLGA) nanoparticles (NPs) of O. acanthium extract (OAE) were synthesized and characterized. It was determined that the average particle size of OAE-PLGA-NPs was 214.9 ± 6.77 nm, and the zeta potential was −8.03 ± 0.85 mV, and PdI value was 0.064 ± 0.013. The encapsulation efficiency of OAE-PLGA-NPs was calculated as 91%, and the loading capacity as 75.83%. The in vitro drug release study showed that OAE was released from the PLGA NPs with 99.39% over the 6 days. Furthermore, the mutagenic and cytotoxic activity of free OAE and OAE-PLGA-NPs were evaluated by the Ames test and MTT test, respectively. Although 0.75 and 0.37 mg/mL free OAE concentrations caused both frameshift mutation and base pair substitution (p < 0.05), the administered OAE–PLGA NP concentrations were not mutagenic. It was determined with the MTT analysis that the doses of 0.75 and 1.5 mg/mL of free OAE had a cytotoxic effect on the L929 fibroblast cell line (p < 0.05), and OAE-PLGA-NPs had no cytotoxic effect. Moreover, the interaction between the OAE and S. aureus was also investigated using the molecular docking analysis method. The molecular docking and molecular dynamics (MD) results were implemented to elucidate the S. aureus MurE inhibition potential of OAE. It was shown that quercetin in the OAE content interacted significantly with the substantial residues in the catalytic pocket of the S. aureus MurE enzyme, and quercetin performed four hydrogen bond interactions corresponding to a low binding energy of −6.77 kcal/mol with catalytic pocket binding residues, which are crucial for the inhibition mechanism of S. aureus MurE. Finally, the bacterial inhibition values of free OAE and OAE–PLGA NPs were determined against S. aureus using a microdilution method. The antibacterial results showed that the inhibition value of the OAE–PLGA NPs was 69%. In conclusion, from the in vitro and in silico results of the nano-sized OAE-PLGA NP formulation produced in this study, it was evaluated that the formulation may be recommended as a safe and effective nano-phyto-drug candidate against S. aureus. creator: Yasemin Budama-Kilinc creator: Bahar Gok creator: Cigdem Cetin Aluc creator: Serda Kecel-Gunduz uri: https://doi.org/10.7717/peerj.15523 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Budama-Kilinc et al. title: Partial substitution of exogenously applied phosphatic fertilizers by phosphate solubilizing bacteria in maize under calcareous soil link: https://peerj.com/articles/15038 last-modified: 2023-06-07 description: Phosphorus (P) availability is the major constrain in obtaining optimum crop yield in calcareous soils due to its precipitation as dicalcium and octacalcium phosphate by reacting with Ca+2 and Mg+2. Therefore, we explored the role of phosphate solubilizing bacteria (without and with PSB @ 2 kg ha−1) in optimizing maize yield and P availability from soluble and insoluble P sources applied @ of 100 kg P2O5 into calcareous soil. PSB inoculation significantly improved maize plant height (5.6%), 1,000 grain weight (11%), dry matter (7.5%), stover (10.8%) and grain yield (6.8%), plant P concentration (10.1%) and uptake (18.6%), extractable P (3.1%), agronomic (48%) and uptake (53%) P use efficiency over un-inoculated plots. Phosphorus application significantly improved maize yield, soil health and agronomic P use efficiency (4.84 times over control); however, its impact was more pronounced when applied as 50% P each from farmyard manure (FYM) and single super phosphate (SSP). On the basis of overall performance, the sources were ranked as 50% FYM + 50% SSP >50% rock phosphate (RP) + 50% SSP > 100% SSP > 75% FYM + 25% SSP > 75% RP +25% SSP > 100% FYM > 100 RP > control. Interactively, a significant and maximum increased over absolute control in most of the soil and plant tested characteristics were observed when 100 kg P2O5 ha−1 was supplemented 50% each as FYM and SSP along with PSB inoculation which was followed by 50% P each as FYM and SSP demonstrating that PSB were effective in enhancing RP solubilization under calcareous soil. Maximum value cost ratio of 3.1 was observed for 50% P each as FYM and SSP + PSB which was similar to 100% P as FYM + PSB and 75% FYM+ 25% SSP + PSB. Therefore, in calcareous soil P shall be amended 50% each as organic and mineral sources with PSB for its efficient utilization and obtaining optimum yield of maize. creator: Hajira creator: Yousaf Jamal creator: Muhammad Adnan creator: Manzoor Ahmad creator: Maria Mussarat creator: Muhammad Hamzah Saleem creator: Beena Saeed creator: Fazli Wahid creator: Rafi Ullah creator: Shah Fahad creator: Baber Ali creator: Imtiaz Khan creator: Sezai Ercisli creator: Kirill S. Golokhvast uri: https://doi.org/10.7717/peerj.15038 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hajira et al.