title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=352 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Gene expression analysis of potato drought-responsive genes under drought stress in potato (Solanum tuberosum L.) cultivars link: https://peerj.com/articles/17116 last-modified: 2024-03-20 description: The potato (Solanum tuberosum L.), an important field crop consumed extensively worldwide, is adversely affected by abiotic stress factors especially drought. Therefore, it is vital to understand the genetic mechanism under drought stress to decrease loose of yield and quality . This trial aimed to screen drought-responsive gene expressions of potato and determine the drought-tolerant potato cultivar. The trial pattern is a completely randomized block design (CRBD) with four replications under greenhouse conditions. Four cultivars (Brooke, Orwell, Vr808, Shc909) were irrigated with four different water regimes (control and three stress conditions), and the gene expression levels of 10 potato genes were investigated. The stress treatments as follows: Control = 100% field capacity; slight drought = 75% field capacity; moderate drought = 50% field capacity, and severe drought 25% field capacity. To understand the gene expression under drought stress in potato genotypes, RT-qPCR analysis was performed and results showed that the genes most associated with drought tolerance were the StRD22 gene, MYB domain transcription factor, StERD7, Sucrose Synthase (SuSy), ABC Transporter, and StDHN1. The StHSP100 gene had the lowest genetic expression in all cultivars. Among the cultivars, the Orwell exhibited the highest expression of the StRD22 gene under drought stress. Overall, the cultivar with the highest gene expression was the Vr808, closely followed by the Brooke cultivar. As a result, it was determined that potato cultivars Orwell, Vr808, and Brooke could be used as parents in breeding programs to develop drought tolerant potato cultivars. creator: Sadettin Çelik uri: https://doi.org/10.7717/peerj.17116 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Çelik title: Gene‒environment interaction effect of hypothalamic‒pituitary‒adrenal axis gene polymorphisms and job stress on the risk of sleep disturbances link: https://peerj.com/articles/17119 last-modified: 2024-03-20 description: BackgroundStudies have shown that chronic exposure to job stress may increase the risk of sleep disturbances and that hypothalamic‒pituitary‒adrenal (HPA) axis gene polymorphisms may play an important role in the psychopathologic mechanisms of sleep disturbances. However, the interactions among job stress, gene polymorphisms and sleep disturbances have not been examined from the perspective of the HPA axis. This study aimed to know whether job stress is a risk factor for sleep disturbances and to further explore the effect of the HPA axis gene × job stress interaction on sleep disturbances among railway workers.MethodsIn this cross-sectional study, 671 participants (363 males and 308 females) from the China Railway Fuzhou Branch were included. Sleep disturbances were evaluated with the Pittsburgh Sleep Quality Index (PSQI), and job stress was measured with the Effort-Reward Imbalance scale (ERI). Generalized multivariate dimensionality reduction (GMDR) models were used to assess gene‒environment interactions.ResultsWe found a significant positive correlation between job stress and sleep disturbances (P < 0.01). The FKBP5 rs1360780-T and rs4713916-A alleles and the CRHR1 rs110402-G allele were associated with increased sleep disturbance risk, with adjusted ORs (95% CIs) of 1.75 [1.38–2.22], 1.68 [1.30–2.18] and 1.43 [1.09–1.87], respectively. However, the FKBP5 rs9470080-T allele was a protective factor against sleep disturbances, with an OR (95% CI) of 0.65 [0.51–0.83]. GMDR analysis indicated that under job stress, individuals with the FKBP5 rs1368780-CT, rs4713916-GG, and rs9470080-CT genotypes and the CRHR1 rs110402-AA genotype had the greatest risk of sleep disturbances.ConclusionsIndividuals carrying risk alleles who experience job stress may be at increased risk of sleep disturbances. These findings may provide new insights into stress-related sleep disturbances in occupational populations. creator: Min Zhao creator: Yuxi Wang creator: Yidan Zeng creator: Huimin Huang creator: Tong Xu creator: Baoying Liu creator: Chuancheng Wu creator: Xiufeng Luo creator: Yu Jiang uri: https://doi.org/10.7717/peerj.17119 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhao et al. title: Laboratory evaluation of a bio-insecticide candidate from tangerine peel extracts against Trialeurodes vaporariorum (Homoptera: Aleyrodidae) link: https://peerj.com/articles/16885 last-modified: 2024-03-19 description: BackgroundThe excessive use of synthetic insecticides in modern agriculture has led to environmental contamination and the development of insect resistance. Also, the prolonged use of chemical insecticides in producing flowers and tomatoes in greenhouses has caused health problems for workers and their offspring. In this study, we analyzed the efficacy of mandarin peel (Citrus reticulata L.) essential oil (EO) as a natural insecticide against greenhouse whitefly (Trieurodes vaporariorum W., Homoptera: Aleyrodidae), a common pest in greenhouse production of different crops.MethodsPetroleum ether (PET) and n-hexane (HEX) were used as solvents to extract essential oil (EO) from tangerine peels.ResultsThe yield of EO was 1.59% and 2.00% (m/m) for PET and HEX, respectively. Additionally, the insect-killing power of EO was tested by checking how many greenhouse whiteflies died at different times. The results showed that PET and HEX extracts of tangerine EO effectively controlled greenhouse whiteflies. Furthermore, with both solvents, a 12.5% (v/v) application was as practical as the commercial insecticide imidacloprid. Further characterization tests with the polarimeter, FTIR, HPLC-RP, and GC-MS showed that the essential oil (EO) contained about 41% (v/v) of d-limonene and that this compound may be responsible for the observed insecticidal properties.ConclusionTherefore, tangerine peel essential oil is an excellent botanical insecticide candidate for controlling greenhouse whiteflies. creator: Nancy Flores creator: Julia Prado creator: Rosario Espin creator: Hortensia Rodríguez creator: José-Manuel Pais-Chanfrau uri: https://doi.org/10.7717/peerj.16885 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Flores et al. title: Overview of chicken embryo genes related to sex differentiation link: https://peerj.com/articles/17072 last-modified: 2024-03-19 description: Sex determination in chickens at an early embryonic stage has been a longstanding challenge in poultry production due to the unique ZZ:ZW sex chromosome system and various influencing factors. This review has summarized the genes related to the sex differentiation of chicken early embryos (mainly Dmrt1, Sox9, Amh, Cyp19a1, Foxl2, Tle4z1, Jun, Hintw, Ube2i, Spin1z, Hmgcs1, Foxd1, Tox3, Ddx4, cHemgn and Serpinb11 in this article), and has found that these contributions enhance our understanding of the genetic basis of sex determination in chickens, while identifying potential gene targets for future research. This knowledge may inform and guide the development of sex screening technologies for hatching eggs and support advancements in gene-editing approaches for chicken embryos. Moreover, these insights offer hope for enhancing animal welfare and promoting conservation efforts in poultry production. creator: Xiaolu Luo creator: Jiancheng Guo creator: Jiahang Zhang creator: Zheng Ma creator: Hua Li uri: https://doi.org/10.7717/peerj.17072 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Luo et al. title: Endosymbiont and gut bacterial communities of the brown-banded cockroach, Supella longipalpa link: https://peerj.com/articles/17095 last-modified: 2024-03-19 description: The brown-banded cockroach (Supella longipalpa) is a widespread nuisance and public health pest. Like the German cockroach (Blattella germanica), this species is adapted to the indoor biome and completes the entirety of its life cycle in human-built structures. Recently, understanding the contributions of commensal and symbiotic microbes to the biology of cockroach pests, as well as the applications of targeting these microbes for pest control, have garnered significant scientific interest. However, relative to B. germanica, the biology of S. longipalpa, including its microbial associations, is understudied. Therefore, the goal of the present study was to quantitatively examine and characterize both the endosymbiont and gut bacterial communities of S. longipalpa for the first time. To do so, bacterial 16S rRNA gene amplicon sequencing was conducted on DNA extracts from whole adult females and males, early instar nymphs, and late instar nymphs. The results demonstrate that the gut microbiome is dominated by two genera of bacteria known to have beneficial probiotic effects in other organisms, namely Lactobacillus and Akkermansia. Furthermore, our data show a significant effect of nymphal development on diversity and variation in the gut microbiome. Lastly, we reveal significant negative correlations between the two intracellular endosymbionts, Blattabacterium and Wolbachia, as well as between Blattabacterium and the gut microbiome, suggesting that Blattabacterium endosymbionts could directly or indirectly influence the composition of other bacterial populations. These findings have implications for understanding the adaptation of S. longipalpa to the indoor biome, its divergence from other indoor cockroach pest species such as B. germanica, the development of novel control approaches that target the microbiome, and fundamental insect-microbe interactions more broadly. creator: Kylene Guse creator: Jose E. Pietri uri: https://doi.org/10.7717/peerj.17095 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Guse and Pietri title: Beliefs, barriers, and promotion practices of Indian nurses’ regarding healthy eating for cancer survivors in a tertiary care hospital—A cross sectional survey link: https://peerj.com/articles/17107 last-modified: 2024-03-19 description: PurposeTo describe the beliefs, barriers and promotion practices of Indian nurses’ regarding healthy eating (HE) behaviours amongst cancer survivors, and to gain insights into whether their educational qualifications might affect the promotion of HE.MethodsData was gathered using a validated questionnaire, 388 of the approached 400 nurses who worked at a tertiary care hospital in India gave informed consent to participate in the study. The Mann-Whitney U test and the Chi square analysis (for continuous and categorical variables respectively) were performed to carry out sub-group comparisons based on the qualification of the nurses i.e., Bachelor of Science in Nursing (BSc) and General Nursing and Midwifery (GNM).ResultsThe nurses believed that dieticians/nutritionists were primarily responsible for educating the cancer survivors regarding HE. HE was promoted by nurses’ relatively equally across multiple treatment stages (“during” treatment 24.4%, “post” treatment 23.1%; and “pre” treatment 22.3%). Nurses’ believed HE practices had numerous benefits, with improved health-related quality of life (HRQoL) (75.7%), and mental health (73.9%) being the most frequent responses. The most frequently cited barriers by the nurses in promoting HE were lack of time (22.2%), and lack of adequate support structure (19.9%). Sub-group comparisons generally revealed no significant difference between the BSc and GNM nurses in their perceptions regarding HE promotion to cancer survivors. Exceptions were how the GNM group had significantly greater beliefs regarding whether HE can “reduce risk of cancer occurrence” (p = 0.004) and “whether or not I promote HE is entirely up to me” (p = 0.002).ConclusionThe nurses in India believe in the promotion of HE practices among cancer survivors across various stages of cancer treatments. However, they do face a range of barriers in their attempt to promote HE. Overcoming these barriers might facilitate effective promotion of HE among cancer survivors and help improve survivorship outcomes.Implications for cancer survivorsIndian nurses employed in the two tertiary care hospitals wish to promote HE among cancer survivors, but require further knowledge and support services for more effective promotion of HE. creator: Hritika D. Pai creator: Stephen Rajan Samuel creator: K. Vijaya Kumar creator: Charu Eapen creator: Alicia Olsen creator: Justin W.L. Keogh uri: https://doi.org/10.7717/peerj.17107 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pai et al. title: TBX5 genetic variants and SCD-CAD susceptibility: insights from Chinese Han cohorts link: https://peerj.com/articles/17139 last-modified: 2024-03-19 description: BackgroundThe prevention and prediction of sudden cardiac death (SCD) present persistent challenges, prompting exploration into common genetic variations for potential insights. T-box 5 (TBX5), a critical cardiac transcription factor, plays a pivotal role in cardiovascular development and function. This study systematically examined variants within the 500-bp region downstream of the TBX5 gene, focusing on their potential impact on susceptibility to SCD associated with coronary artery disease (SCD-CAD) in four different Chinese Han populations.MethodsIn a comprehensive case-control analysis, we explored the association between rs11278315 and SCD-CAD susceptibility using a cohort of 553 controls and 201 SCD-CAD cases. Dual luciferase reporter assays and genotype-phenotype correlation studies using human cardiac tissue samples as well as integrated in silicon analysis were applied to explore the underlining mechanism.ResultBinary logistic regression results underscored a significantly reduced risk of SCD-CAD in individuals harboring the deletion allele (odds ratio = 0.70, 95% CI [0.55–0.88], p = 0.0019). Consistent with the lower transcriptional activity of the deletion allele observed in dual luciferase reporter assays, genotype-phenotype correlation studies on human cardiac tissue samples affirmed lower expression levels associated with the deletion allele at both mRNA and protein levels. Furthermore, our investigation revealed intriguing insights into the role of rs11278315 in TBX5 alternative splicing, which may contribute to alterations in its ultimate functional effects, as suggested by sQTL analysis. Gene ontology analysis and functional annotation further underscored the potential involvement of TBX5 in alternative splicing and cardiac-related transcriptional regulation.ConclusionsIn summary, our current dataset points to a plausible correlation between rs11278315 and susceptibility to SCD-CAD, emphasizing the potential of rs11278315 as a genetic risk marker for aiding in molecular diagnosis and risk stratification of SCD-CAD. creator: Yukun Rui creator: Ju Zhou creator: Xiaoyuan Zhen creator: Jianhua Zhang creator: Shiquan Liu creator: Yuzhen Gao uri: https://doi.org/10.7717/peerj.17139 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rui et al. title: Biochar’s role in improving pakchoi quality and microbial community structure in rhizosphere soil link: https://peerj.com/articles/16733 last-modified: 2024-03-18 description: BackgroundBiochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi (Brassica campestris L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes.MethodsThe soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq.ResultsThe results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, Gemmatimonadetes, Anaerolineae, Deltaproteobacteria and Verrucomicrobiae were reduced, and Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, and Acidimicrobiia relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of Gemmatimonas and increased the relative abundances of Ilumatobacter, Luteolibacter, Lysobacter, Arthrobacter, and Mesorhizobium. The nitrate content was positively correlated with the abundance of Gemmatimonadetes, and the nitrate content was significantly negatively correlated with the relative abundance of Ilumatobacter. Carbohydrate transport and metabolism in the rhizosphere soil of pakchoi decreased, and lipid transport and metabolism increased after biochar application.ConclusionOverall, our results indicated that applying biochar improved soil physicochemical states and plant nutrient absorption, and affected the abundance of dominant bacterial groups (e.g., Gemmatimonadetes and Ilumatobacter), these were the main factors to increase pakchoi growth and promote quality of pakchoi. Therefore, considering the growth, quality of pakchoi, and soil environment, the effect of using 3% biochar is better. creator: Xia Wu creator: Fengjun Yang creator: Jili Zhang creator: Feng Gao creator: Yi Chen Hu creator: Kejun Yang creator: Peng Wang uri: https://doi.org/10.7717/peerj.16733 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Wu et al. title: Anti-ENO1 antibody combined with metformin against tumor resistance: a novel antibody-based platform link: https://peerj.com/articles/16817 last-modified: 2024-03-18 description: BackgroundAntibody-based platforms (i.e., ADC) have emerged as one of the most encouraging tools for the cancer resistance caused by cancer stem cells (CSCs) enrichment. Our study might provide a promising therapeutic direction against drug resistance and serve as a potential precursor platform for screening ADC.MethodsThe cell migration, invasion, drug resistance, and self-renewal were assessed by the cell invasion and migration assay, wound healing assay, CCK-8 assay, colony formation assay, and sphere formation assay, respectively. The expression profiles of CSCs (ALDH+ and CD44+) subpopulations were screened by flow cytometry. The western blot and cell immunofluorescence assay were used to evaluate pathway-related protein expression in both anti-ENO1 antibody, MET combined with DPP/CTX-treated CSCs.ResultsIn the present study, western blot and flow cytometry verified that anti-ENO1 antibody target the CD44+ subpopulation by inhibiting the PI3K/AKT pathway, while metformin might target the ALDH+ subpopulation through activation of the AMPK pathway and thus reverse drug resistance to varying degrees. Subsequently, in vitro investigation indicated that anti-ENO1 antibody, metformin combined with cisplatin/cetuximab could simultaneously target ALDH+ and CD44+ subpopulations. The combination also inhibited the CSCs proliferation, migration, invasion, and sphere formation; which may result in overcoming the drug resistance. Then, molecular mechanism exploration verified that the anti-ENO1 antibody, metformin combined with cisplatin/cetuximab inhibited the Wnt/β-catenin signaling.ConclusionsThe study preliminarily revealed anti-ENO1 antibody combined with metformin could overcome drug resistance against CSCs by inhibiting the Wnt//β-catenin pathway and might serve as a potential precursor platform for screening ADC. More importantly, it is reasonably believed that antibody-based drug combination therapy might function as an encouraging tool for oncotherapy. creator: Xiong Shu creator: Hui Wen Zhang creator: Shi Ya Liu creator: Li Xin Sun creator: Tao Zhang creator: Yu Liang Ran uri: https://doi.org/10.7717/peerj.16817 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Shu et al. title: Integrating single-cell and bulk sequencing data to identify glycosylation-based genes in non-alcoholic fatty liver disease-associated hepatocellular carcinoma link: https://peerj.com/articles/17002 last-modified: 2024-03-18 description: BackgroundThe incidence of non-alcoholic fatty liver disease (NAFLD) associated hepatocellular carcinoma (HCC) has been increasing. However, the role of glycosylation, an important modification that alters cellular differentiation and immune regulation, in the progression of NAFLD to HCC is rare.MethodsWe used the NAFLD-HCC single-cell dataset to identify variation in the expression of glycosylation patterns between different cells and used the HCC bulk dataset to establish a link between these variations and the prognosis of HCC patients. Then, machine learning algorithms were used to identify those glycosylation-related signatures with prognostic significance and to construct a model for predicting the prognosis of HCC patients. Moreover, it was validated in high-fat diet-induced mice and clinical cohorts.ResultsThe NAFLD-HCC Glycogene Risk Model (NHGRM) signature included the following genes: SPP1, SOCS2, SAPCD2, S100A9, RAMP3, and CSAD. The higher NHGRM scores were associated with a poorer prognosis, stronger immune-related features, immune cell infiltration and immunity scores. Animal experiments, external and clinical cohorts confirmed the expression of these genes.ConclusionThe genetic signature we identified may serve as a potential indicator of survival in patients with NAFLD-HCC and provide new perspectives for elucidating the role of glycosylation-related signatures in this pathologic process. creator: Zhijia Zhou creator: Yanan Gao creator: Longxin Deng creator: Xiaole Lu creator: Yancheng Lai creator: Jieke Wu creator: Shaodong Chen creator: Chengzhong Li creator: Huiqing Liang uri: https://doi.org/10.7717/peerj.17002 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Zhou et al.