Pan-cancer analysis identifies olfactory receptor family 7 subfamily A member 5 as a potential biomarker for glioma
Background Human olfactory receptors (ORs) account for approximately 60% of all human G protein-coupled receptors. The functions of ORs extend beyond olfactory perception and have garnered significant attention in tumor biology. However, a comprehensive pan-cancer analysis of ORs in human cancers is lacking. Methods Using data from public databases, such as HPA, TCGA, GEO, GTEx, TIMER2, TISDB, UALCAN, GEPIA2, and GSCA, this study investigated the role of olfactory receptor family 7 subfamily A member 5 (OR7A5) in various cancers. Functional analysis of OR7A5 in LGG and GBM was performed using the CGGA database. Molecular and cellular experiments were performed to validate the expression and biological function of OR7A5 in gliomas. Results The results revealed heightened OR7A5 expression in certain tumors, correlating with the expression levels of immune checkpoints and immune infiltration. In patients with gliomas, the expression levels of OR7A5 were closely associated with adverse prognosis, 1p/19p co-deletion status, and wild-type IDH status. Finally, in vitro experiments confirmed the inhibitory effect of OR7A5 knockdown on the proliferative capacity of glioma cells and on the expression levels of proteins related to lipid metabolism. Conclusion This study establishes OR7A5 as a novel biomarker, potentially offering a novel therapeutic target for gliomas.
Bao et al. (2024) Pan-cancer analysis identifies olfactory receptor family 7 subfamily A member 5 as a potential biomarker for glioma. PeerJ 12:e17631 https://doi.org/10.7717/peerj.17631
The potential role of CD8+ cytotoxic T lymphocytes and one branch connected with tissue-resident memory in non-luminal breast cancer
Advances in understanding the pathological mechanisms of breast cancer have resulted in the emergence of novel therapeutic strategies. However, triple-negative breast cancer (TNBC), a molecular subtype of breast cancer with a poor prognosis, lacks classical and general therapeutic targets, hindering the clinical application of several therapies to breast cancer. As insights into the unique immunity and molecular mechanisms of TNBC have become more extensive, immunotherapy has gradually become a valuable complementary approach to classical radiotherapy and chemotherapy. CD8+ cells are significant actors in the tumor immunity cycle; thus, research on TNBC immunotherapy is increasingly focused in this direction. Recently, CD8+ tissue-resident memory (TRM) cells, a subpopulation of CD8+ cells, have been explored in relation to breast cancer and found to seemingly play an undeniably important role in tumor surveillance and lymphocytic infiltration. In this review, we summarize the recent advances in the mechanisms and relative targets of CD8+ T cells, and discuss the features and potential applications of CD8+ TRM cells in non-luminal breast cancer immunotherapy.
Zhao et al. (2024) The potential role of CD8+ cytotoxic T lymphocytes and one branch connected with tissue-resident memory in non-luminal breast cancer. PeerJ 12:e17667 https://doi.org/10.7717/peerj.17667
The osteology of the wrist of Heyuannia huangi (Oviraptorosauria) and its implications for the wrist folding mechanism
The wrist of extant birds is highly specialized which permits folding of the forelimb in order to protect the pennaceous feathers when they are relaxed. This mechanism is absent in most non-avian theropods and is unknown in oviraptorosaurs because of the rarity of the specimens with well-preserved wrist. Here we give a detailed description of the wrist of two three-dimensionally preserved oviraptorosaurian Heyuannia huangi specimens from the Upper Cretaceous in Southern China. Heyuannia huangi possesses a highly specialized wrist with a strongly dorsoventrally compressed distal ulna, a larger radiale angle and a strongly convex semilunate carpal. The morphology of its wrist suggests that the distal ulna would not hinder the rotation of the manus, resulting in the smallest angle between the manus and the ulna being less than 90 degrees. The combination of the morphology of the wrist of oviraptorosaurs and the phylogenetic result indicates functional convergence in the wrist of oviraptorids and extant birds.
Qiu et al. (2024) The osteology of the wrist of Heyuannia huangi (Oviraptorosauria) and its implications for the wrist folding mechanism. PeerJ 12:e17669 https://doi.org/10.7717/peerj.17669
Molecular insights into programmed cell death in esophageal squamous cell carcinoma
Background Esophageal squamous cell carcinoma (ESCC) is a deadly type of esophageal cancer. Programmed cell death (PCD) is an important pathway of cellular self-extermination and is closely involved in cancer progression. A detailed study of its mechanism may contribute to ESCC treatment. Methods We obtained expression profiling data of ESCC patients from public databases and genes related to 12 types of PCD from previous studies. Hub genes in ESCC were screened from PCD-related genes applying differential expression analysis, machine learning analysis, linear support vector machine (SVM), random forest and Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis. In addition, based on the HTFtarget and TargetScan databases, transcription factors (TFs) and miRNAs interacting with the hub genes were selected. The relationship between hub genes and immune cells were analyzed using the CIBERSORT algorithm. Finally, to verify the potential impact of the screened hub genes on ESCC occurrence and development, a series of in vitro cell experiments were conducted. Results We screened 149 PCD-related DEGs, of which five DEGs (INHBA, LRRK2, HSP90AA1, HSPB8, and EIF2AK2) were identified as the hub genes of ESCC. The area under the curve (AUC) of receiver operating characteristic (ROC) curve of the integrated model developed using the hub genes reached 0.997, showing a noticeably high diagnostic accuracy. The number of TFs and miRNAs regulating hub genes was 105 and 22, respectively. INHBA, HSP90AA1 and EIF2AK2 were overexpressed in cancer tissues and cells of ESCC. Notably, INHBA knockdown suppressed ECSS cell migration and invasion and altered the expression of important apoptotic and survival proteins. Conclusion This study identified significant molecules with promising accuracy for the diagnosis of ESCC, which may provide a new perspective and experimental basis for ESCC research.
Chen et al. (2024) Molecular insights into programmed cell death in esophageal squamous cell carcinoma. PeerJ 12:e17690 https://doi.org/10.7717/peerj.17690
Predator in proximity: how does a large carnivore respond to anthropogenic pressures at fine-scales? Implications for interface area management
Background Driven by habitat loss and fragmentation, large carnivores are increasingly navigating human-dominated landscapes, where their activity is restricted and their behaviour altered. This movement, however, raises significant concerns and costs for people living nearby. While intricately linked, studies often isolate human and carnivore impacts, hindering effective management efforts. Hence, in this study, we brought these two into a common framework, focusing on an interface area between the critical tiger habitat and the human-dominated multiple-use buffer area of a central Indian protected area. Methods We employed a fine-scale camera trap survey complemented by GPS-collar movement data to understand spatio-temporal activity patterns and adjustments of tigers in response to anthropogenic pressures. We used an occupancy framework to evaluate space use, Bayesian circular GLMs to model temporal activity, and home range and step length analyses to assess the movement patterns of tigers. Further, we used predation-risk models to understand conflict patterns as a function of tiger presence and other habitat variables. Results Despite disturbance, a high proportion of the sampled area was occupied by 17 unique tigers (ψ = 0.76; CI [0.73–0.92]). The distance to villages (β ± SE = 0.63 ± 0.21) and the relative abundance of large-bodied wild prey (β ± SE = 0.72 ± 0.37) emerged as key predictors of tiger space use probability, indicating a preference for wild prey by tigers, while human influences constrained their habitat utilisation. Distance to villages was also identified as the most significant predictor of the tigers’ temporal activity (μ ± σ = 3.03 ± 0.06 rad) that exhibited higher nocturnality near villages. A total of 11% of tiger home ranges were within village boundaries, accompanied by faster movement in these areas (displacement 40–82% higher). Livestock depredation probability by tigers increased with proximity to villages (P = 0.002) and highway (P = 0.003). Although tiger space use probability (P = 0.056) and wild prey abundance (P = 0.134) were non-significant at the 0.05 threshold, their presence in the best-fit predation-risk model suggests their contextual relevance for understanding conflict risk. The results highlight the importance of appropriately managing livestock near human infrastructures to effectively mitigate conflict. Conclusions Shared space of carnivores and humans requires dynamic site-specific actions grounded in evidence-based decision-making. This study emphasises the importance of concurrently addressing the intricate interactions between humans and large carnivores, particularly the latter’s behavioural adaptations and role in conflict dynamics. Such an integrated approach is essential to unravel cause-effect relationships and promote effective interface management in human-dominated landscapes.
Mohan et al. (2024) Predator in proximity: how does a large carnivore respond to anthropogenic pressures at fine-scales? Implications for interface area management. PeerJ 12:e17693 https://doi.org/10.7717/peerj.17693
Unraveling habitat-driven shifts in alpha, beta, and gamma diversity of hummingbirds and their floral resource
Background Biodiversity, crucial for understanding ecosystems, encompasses species richness, composition, and distribution. Ecological and environmental factors, such as habitat type, resource availability, and climate conditions, play pivotal roles in shaping species diversity within and among communities, categorized into alpha (within habitat), beta (between habitats), and gamma (total regional) diversity. Hummingbird communities are influenced by habitat, elevation, and seasonality, making them an ideal system for studying these diversities, shedding light on mutualistic community dynamics and conservation strategies. Methods Over a year-long period, monthly surveys were conducted to record hummingbird species and their visited flowering plants across four habitat types (oak forest, juniper forest, pine forest, and xerophytic shrubland) in Tlaxcala, Mexico. Three locations per habitat type were selected based on conservation status and distance from urban areas. True diversity measures were used to assess alpha, beta, and gamma diversity of hummingbirds and their floral resources. Environmental factors such as altitude and bioclimatic variables were explored for their influence on beta diversity. Results For flowering plants, gamma diversity encompassed 34 species, with oak forests exhibiting the highest richness, while xerophytic shrublands had the highest alpha diversity. In contrast, for hummingbirds, 11 species comprised the gamma diversity, with xerophytic shrublands having the highest richness and alpha diversity. Our data reveal high heterogeneity in species abundance among habitats. Notably, certain floral resources like Loeselia mexicana and Bouvardia ternifolia emerge as key species in multiple habitats, while hummingbirds such as Basilinna leucotis, Selasphorus platycercus, and Calothorax lucifer exhibit varying levels of abundance and habitat preferences. Beta diversity analyses unveil habitat-specific patterns, with species turnover predominantly driving dissimilarity in composition. Moreover, our study explores the relationships between these diversity components and environmental factors such as altitude and climate variables. Climate variables, in particular, emerge as significant contributors to dissimilarity in floral resource and hummingbird communities, highlighting the influence of environmental conditions on species distribution. Conclusions Our results shed light on the complex dynamics of hummingbird-flower mutualistic communities within diverse habitats and underscore the importance of understanding how habitat-driven shifts impact alpha, beta, and gamma diversity. Such insights are crucial for conservation strategies aimed at preserving the delicate ecological relationships that underpin biodiversity in these communities.
Martínez-Roldán et al. (2024) Unraveling habitat-driven shifts in alpha, beta, and gamma diversity of hummingbirds and their floral resource. PeerJ 12:e17713 https://doi.org/10.7717/peerj.17713
Comparative analysis of nutrient composition and antioxidant activity in three dragon fruit cultivars
Dragon fruit has significant economic value in many countries due to has excellent nutritional content, health advantages, and adaptability to different climates, making it an important crop in the global fruit industry. This study aimed to gather comprehensive nutritional data on three dragon fruit cultivars by analysing the levels of micronutrients, fibre, carbohydrates, antioxidants, vitamins, and minerals in their pulps. Uniform dragon fruit samples underwent thorough analysis for proximate composition, mineral content, pigments, antioxidants, and vitamin C, with statistical methods used to assess significant differences among the parameters studied. The proximate composition analysis revealed significant differences among the three dragon fruit cultivars. Among the proximate components, protein (0.40 ± 0.02 g/100 g), moisture (91.33 ± 0.88%), crude fibre (0.32 ± 0.07 g/100 g), and ash (1.27 ± 0.09 g/100 g) were more abundant in Hylocereus costaricensis than in Hylocereus undatus and Hylocereus megalanthus. On the other hand, Hylocereus undatus had higher carbohydrate (17.02 ± 0.63 g/100 g) and energy (69.74 ± 2.44 kcal/100 g) contents. K (7.23 ± 0.35 mg/100 g), Ca (1.61 ± 0.13 mg/100 g), Fe (1.84 ± 0.05 mg/100 g), and Zn (0.37 ± 0.034 mg/100 g) are highly abundant in H. costaricensis. Additionally, Hylocereus costaricensis had the highest anthocyanin content (120.15 ± 3.29 mg/g FW) and total carotenoid content (72.51 ± 1.62 mg/g FW), along with the highest vitamin C content (8.92 ± 0.13 mg/g FW) and total soluble phenolic content (572.48 ± 20.77 mg/100 g). Its remarkable antioxidant activity was further highlighted by the lowest SC50 value (13.50 ± 0.4 mg/mL) for its DPPH radical scavenging capacity. The total soluble sugar content was highest in Hylocereus megalanthus (8.72 ± 0.30 g/100 g FW). Hierarchical clustering analysis revealed distinct trait and genotype associations; among the studied cultivars, Hylocereus costaricensis demonstrated superior performance across multiple traits. Correlation analysis indicated significant positive correlations among several traits, while principal component analysis highlighted the contribution of each trait to overall variance, with PC1 explaining 73.95% of the total variance. This study highlights the nutritional variations among dragon fruit cultivars, with Hylocereus costaricensis showing superior performance, guiding dietary planning and functional food development.
Yasmin et al. (2024) Comparative analysis of nutrient composition and antioxidant activity in three dragon fruit cultivars. PeerJ 12:e17719 https://doi.org/10.7717/peerj.17719
Ginkgetin attenuates bone loss in OVX mice by inhibiting the NF-κB/IκBα signaling pathway
Background Osteoporosis is a disease associated with bone resorption, characterized primarily by the excessive activation of osteoclasts. Ginkgetin is a compound purified from natural ginkgo leaves which has various biological properties, including anti-inflammation, antioxidant, and anti-tumor effects. This study investigated the bone-protective effects of ginkgetin in ovariectomized (OVX) mice and explored their potential signaling pathway in inhibiting osteoclastogenesis in a mouse model of osteoporosis. Methods Biochemical assays were performed to assess the levels of Ca, ALP, and P in the blood. Micro CT scanning was used to evaluate the impact of ginkgetin on bone loss in mice. RT-PCR was employed to detect the expression of osteoclast-related genes (ctsk, c-fos, trap) in their femoral tissue. Hematoxylin and eosin (H&E) staining was utilized to assess the histopathological changes in femoral tissue due to ginkgetin. The TRAP staining was used to evaluate the impact of ginkgetin osteoclast generation in vivo. Western blot analysis was conducted to investigate the effect of ginkgetin on the expression of p-NF-κB p65 and IκBα proteins in mice. Results Our findings indicate that ginkgetin may increase the serum levels of ALP and P, while decreasing the serum level of Ca in OVX mice. H&E staining and micro CT scanning results suggest that ginkgetin can inhibit bone loss in OVX mice. The TRAP staining results showed ginkgetin suppresses the generation of osteoclasts in OVX mice. RT-PCR results demonstrate that ginkgetin downregulate the expression of osteoclast-related genes (ctsk, c-fos, trap) in the femoral tissue of mice, and this effect is dose-dependent. Western blot analysis results reveal that ginkgetin can inhibit the expression of p-NF-κB p65 and IκBα proteins in mice. Conclusion Ginkgetin can impact osteoclast formation and activation in OVX mice by inhibiting the NF-κB/IκBα signaling pathway, thereby attenuating bone loss in mice.
Wei et al. (2024) Ginkgetin attenuates bone loss in OVX mice by inhibiting the NF-κB/IκBα signaling pathway. PeerJ 12:e17722 https://doi.org/10.7717/peerj.17722
Endophytic actinomycetes promote growth and fruits quality of tomato (Solanum lycopersicum): an approach for sustainable tomato production
Background Tomato, a fruit with a high vitamin content, is popular for consumption and economically important in Thailand. However, in the past year, the extensive usage of chemicals has significantly decreased tomato yields. Plant Growth-Promoting Rhizobacteria (PGPR) is an alternative that can help improve tomato production system growth and yield quality while using fewer chemicals. The present study aimed to determine whether endophytic actinomycetes promote growth and fruit quality of tomato (Solanum lycopersicum). Methods The experiment was conducted in a net-houses at the Center for Agricultural Resource System Research, Faculty of Agriculture, Chiang Mai University, Chiang Mai province, Thailand. The randomized completely block design (RCBD) was carried out for four treatments with three replications, which was control, inoculation with TGsR-03-04, TGsL-02-05 and TGsR-03-04 with TGsL-02-05 in tomato plant. Isolated Actinomycetes spp. of each treatment was then inoculated into the root zone of tomato seedlings and analyzed by Scanning Electron Microscopy (SEM). The height of tomato plants was measured at 14, 28, 56, and 112 days after transplanting. Final yield and yield quality of tomato was assessed at the maturity phase. Results The SEM result illustrated that the roots of tomato seedlings from all treatments were colonized by endophytic actinomycetes species. This contributed to a significant increase in plant height at 14 days after transplanting (DAT), as found in the TGsR-03-04 treatment (19.40 cm) compared to the control. Besides, all inoculated treatments enhanced tomato yield and yield quality. The highest weight per fruit (47.38 g), fruit length (52.37 mm), vitamin C content (23.30 mg 100 g−1), and lycopene content (145.92 µg g−1) were obtained by inoculation with TGsR-03-04. Moreover, the highest yield (1.47 kg plant−1) was obtained by inoculation with TGsL-02-05. There was no statistically significant difference in the number of fruits per plant, fruit width, brix, and antioxidant activity when various inoculations of endophytic actinomycetes were applied. Therefore, the use of endophytic actinomycetes in tomato cultivation may be an alternative to increase tomato yield and yield quality.
Khomampai et al. (2024) Endophytic actinomycetes promote growth and fruits quality of tomato (Solanum lycopersicum): an approach for sustainable tomato production. PeerJ 12:e17725 https://doi.org/10.7717/peerj.17725
Investigating the regulatory role of HvANT2 in anthocyanin biosynthesis through protein–motif interaction in Qingke
Background Currently, there are no reports on the HvbHLH gene family in the recent barley genome (Morex_V3). Furthermore, the structural genes related to anthocyanin synthesis that interact with HvANT2 have yet to be fully identified. Methods In this study, a bioinformatics approach was used to systematically analyze the HvbHLH gene family. The expression of this gene family was analyzed through RNA sequencing (RNA-seq), and the gene with the most significant expression level, HvANT2, was analyzed using quantitative reverse transcription polymerase chain reaction (qRT-PCR) in different tissues of two differently colored varieties. Finally, structural genes related to anthocyanin synthesis and their interactions with HvANT2 were verified using a yeast one-hybrid (Y1H) assay. Results The study identified 161 bHLH genes, designated as HvbHLH1 to HvbHLH161, from the most recent barley genome available. Evolutionary tree analysis categorized barley bHLH TFs into 21 subfamilies, demonstrating a pronounced similarity to rice and maize. Through RNA-Seq analysis of purple and white grain Qingke, we discovered a significant transcription factor (TF), HvANT2 (HvbHLH78), associated with anthocyanin biosynthesis. Subsequently, HvANT2 protein-motifs interaction assays revealed 41 interacting motifs, three of which were validated through Y1H experiments. These validated motifs were found in the promoter regions of key structural genes (CHI, F3’H, and GT) integral to the anthocyanin synthesis pathway. These findings provide substantial evidence for the pivotal role of HvANT2 TF in anthocyanin biosynthesis.
Wang et al. (2024) Investigating the regulatory role of HvANT2 in anthocyanin biosynthesis through protein–motif interaction in Qingke. PeerJ 12:e17736 https://doi.org/10.7717/peerj.17736