title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=327 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Transcriptome differential expression analysis of defoliation of two different lemon varieties link: https://peerj.com/articles/17218 last-modified: 2024-04-26 description: ‘Allen Eureka’ is a bud variety of Eureka lemon with excellent fruiting traits. However, it suffers from severe winter defoliation that leads to a large loss of organic nutrients and seriously affects the tree’s growth and development as well as the yield of the following year, and the mechanism of its response to defoliation is still unclear. In order to investigate the molecular regulatory mechanisms of different leaf abscission periods in lemon, two lemon cultivars (‘Allen Eureka’ and ‘Yunning No. 1’) with different defoliation traits were used as materials. The petiole abscission zone (AZ) was collected at three different defoliation stages, namely, the pre-defoliation stage (CQ), the mid-defoliation stage (CZ), and the post-defoliation stage (CH). Transcriptome sequencing was performed to analyze the gene expression differences between these two cultivars. A total of 898, 4,856, and 3,126 differentially expressed genes (DEGs) were obtained in CQ, CZ, and CH, respectively, and the number of DEGs in CZ was the largest. GO analysis revealed that the DEGs between the two cultivars were mainly enriched in processes related to oxidoreductase, hydrolase, DNA binding transcription factor, and transcription regulator activity in the defoliation stages. KEGG analysis showed that the DEGs were concentrated in CZ and involved plant hormone signal transduction, phenylpropanoid biosynthesis, glutathione metabolism, and alpha-linolenic acid metabolism. The expression trends of some DEGs suggested their roles in regulating defoliation in lemon. Eight gene families were obtained by combining DEG clustering analysis and weighted gene co-expression network analysis (WGCNA), including β-glucosidase, AUX/IAA, SAUR, GH3, POD, and WRKY, suggesting that these genes may be involved in the regulation of lemon leaf abscission. The above conclusions enrich the research related to lemon leaf abscission and provide reliable data for the screening of lemon defoliation candidate genes and analysis of defoliation pathways. creator: Meichao Dong creator: Tuo Yin creator: Junyan Gao creator: Hanyao Zhang creator: Fan Yang creator: Shaohua Wang creator: Chunrui Long creator: Xiaomeng Fu creator: Hongming Liu creator: Lina Guo creator: Dongguo Zhou uri: https://doi.org/10.7717/peerj.17218 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Dong et al. title: Microbial communities of Schisandra sphenanthera Rehd. et Wils. and the correlations between microbial community and the active secondary metabolites link: https://peerj.com/articles/17240 last-modified: 2024-04-26 description: BackgroundSchisandra sphenanthera Rehd. et Wils. is a plant used in traditional Chinese medicine (TCM). However, great differences exist in the content of active secondary metabolites in various parts of S. sphenanthera. Do microorganisms critically influence the accumulation of active components in different parts of S. sphenanthera?MethodsIn this study, 16S/ITS amplicon sequencing analysis was applied to unravel microbial communities in rhizospheric soil and different parts of wild S. sphenanthera. At the same time, the active secondary metabolites in different parts were detected, and the correlation between the secondary metabolites and microorganisms was analyzed.ResultsThe major components identified in the essential oils were sesquiterpene and oxygenated sesquiterpenes. The contents of essential oil components in fruit were much higher than that in stem and leaf, and the dominant essential oil components were different in these parts. The dominant components of the three parts were γ-muurolene, δ-cadinol, and trans farnesol (stem); α-cadinol and neoisolongifolene-8-ol (leaf); isosapathulenol, α-santalol, cedrenol, and longiverbenone (fruit). The microbial amplicon sequences were taxonomically grouped into eight (bacteria) and seven (fungi) different phyla. Community diversity and composition analyses showed that different parts of S. sphenanthera had similar and unique microbial communities, and functional prediction analysis showed that the main functions of microorganisms were related to metabolism. Moreover, the accumulation of secondary metabolites in S. sphenanthera was closely related to the microbial community composition, especially bacteria. In endophytic bacteria, Staphylococcus and Hypomicrobium had negative effects on five secondary metabolites, among which γ-muurolene and trans farnesol were the dominant components in the stem. That is, the dominant components in stems were greatly affected by microorganisms. Our results provided a new opportunity to further understand the effects of microorganisms on the active secondary metabolites and provided a basis for further research on the sustainable utilization of S. sphenanthera. creator: Xiaolu Qin creator: Han Pu creator: Xilin Fang creator: Qianqian Shang creator: Jianhua Li creator: Qiaozhu Zhao creator: Xiaorui Wang creator: Wei Gu uri: https://doi.org/10.7717/peerj.17240 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Qin et al. title: Influence of honey bee (Apis mellifera) breeding on wing venation in Serbia and neighbouring countries link: https://peerj.com/articles/17247 last-modified: 2024-04-26 description: In order to improve the productivity of honey bees (Apis mellifera), some of their traits are selected by breeding. On one hand, breeding is mainly based on the natural geographical variation of this species; on the other hand, mass production and distribution of artificially selected queens can significantly affect the natural geographic variation of honey bees. In this study, we have compared honey bee wings originating from breeding and non-breeding populations in Serbia. In the comparison, we have also used data from a large area of south-eastern Europe. The wings were measured using the 19 landmarks indicated on the wing images. The coordinates were analysed using the methodology of geometric morphometrics. We found that honey bees obtained from honey bee queen breeder differed in wing venation from surrounding populations, which are under natural selection. Therefore, we argue against including populations under artificial selection in the analysis of the natural geographical variation of honey bees. In our analysis of non-breeding samples, we found that in south-eastern Europe there is continuous variation in wing venation and no clear boundaries between A. m. carnica, A. m. cecropia, and A. m. macedonica. creator: Hardeep Kaur creator: Nebojša Nedić creator: Adam Tofilski uri: https://doi.org/10.7717/peerj.17247 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Kaur et al. title: Genome-wide identification and analysis of ascorbate peroxidase (APX) gene family in hemp (Cannabis sativa L.) under various abiotic stresses link: https://peerj.com/articles/17249 last-modified: 2024-04-26 description: Ascorbate peroxidase (APX) plays a critical role in molecular mechanisms such as plant development and defense against abiotic stresses. As an important economic crop, hemp (Cannabis sativa L.) is vulnerable to adverse environmental conditions, such as drought, cold, salt, and oxidative stress, which lead to a decline in yield and quality. Although APX genes have been characterized in a variety of plants, members of the APX gene family in hemp have not been completely identified. In this study, we (1) identified eight members of the CsAPX gene family in hemp and mapped their locations on the chromosomes using bioinformatics analysis; (2) examined the physicochemical characteristics of the proteins encoded by these CsAPX gene family members; (3) investigated their intraspecific collinearity, gene structure, conserved domains, conserved motifs, and cis-acting elements; (4) constructed a phylogenetic tree and analyzed interspecific collinearity; and (5) ascertained expression differences in leaf tissue subjected to cold, drought, salt, and oxidative stresses using quantitative real-time-PCR (qRT-PCR). Under all four stresses, CsAPX6, CsAPX7, and CsAPX8 consistently exhibited significant upregulation, whereas CsAPX2 displayed notably higher expression levels under drought stress than under the other stresses. Taken together, the results of this study provide basic genomic information on the expression of the APX gene family and pave the way for studying the role of APX genes in abiotic stress. creator: Zixiao Liang creator: Hongguo Xu creator: Hongying Qi creator: Yiying Fei creator: Jiaying Cui uri: https://doi.org/10.7717/peerj.17249 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liang et al. title: A CT-based integrated model for preoperative prediction of occult lymph node metastasis in early tongue cancer link: https://peerj.com/articles/17254 last-modified: 2024-04-26 description: BackgroundOccult lymph node metastasis (OLNM) is an essential prognostic factor for early-stage tongue cancer (cT1-2N0M0) and a determinant of treatment decisions. Therefore, accurate prediction of OLNM can significantly impact the clinical management and outcomes of patients with tongue cancer. The aim of this study was to develop and validate a multiomics-based model to predict OLNM in patients with early-stage tongue cancer.MethodsThe data of 125 patients diagnosed with early-stage tongue cancer (cT1-2N0M0) who underwent primary surgical treatment and elective neck dissection were retrospectively analyzed. A total of 100 patients were randomly assigned to the training set and 25 to the test set. The preoperative contrast-enhanced computed tomography (CT) and clinical data on these patients were collected. Radiomics features were extracted from the primary tumor as the region of interest (ROI) on CT images, and correlation analysis and the least absolute shrinkage and selection operator (LASSO) method were used to identify the most relevant features. A support vector machine (SVM) classifier was constructed and compared with other machine learning algorithms. With the same method, a clinical model was built and the peri-tumoral and intra-tumoral images were selected as the input for the deep learning model. The stacking ensemble technique was used to combine the multiple models. The predictive performance of the integrated model was evaluated for accuracy, sensitivity, specificity, and the area under the receiver operating characteristic curve (AUC-ROC), and compared with expert assessment. Internal validation was performed using a stratified five-fold cross-validation approach.ResultsOf the 125 patients, 41 (32.8%) showed OLNM on postoperative pathological examination. The integrated model achieved higher predictive performance compared with the individual models, with an accuracy of 84%, a sensitivity of 100%, a specificity of 76.5%, and an AUC-ROC of 0.949 (95% CI [0.870–1.000]). In addition, the performance of the integrated model surpassed that of younger doctors and was comparable to the evaluation of experienced doctors.ConclusionsThe multiomics-based model can accurately predict OLNM in patients with early-stage tongue cancer, and may serve as a valuable decision-making tool to determine the appropriate treatment and avoid unnecessary neck surgery in patients without OLNM. creator: Wei Han creator: Yingshu Wang creator: Tao Li creator: Yuke Dong creator: Yanwei Dang creator: Liang He creator: Lianfang Xu creator: Yuhao Zhou creator: Yujie Li creator: Xudong Wang uri: https://doi.org/10.7717/peerj.17254 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Han et al. title: The status and influencing factors of abnormal fetal pregnancy outcomes in 265 cases in China: a retrospective study link: https://peerj.com/articles/17284 last-modified: 2024-04-26 description: BackgroundWith the advancement of prenatal diagnosis technology, the detection rate of fetal abnormalities continues to increase, imposing a significant burden on both society and families. A retrospective analysis of essential information about pregnant women, such as their pregnancy history and delivery details, is crucial for understanding the primary factors that influence pregnancy outcomes in women with fetal abnormalities. This analysis is of great significance for improving the level of pregnancy management and outcomes in pregnant women with fetal abnormalities.ObjectiveTo retrospectively analyze the pregnancy outcomes of women with fetal abnormalities and explore the factors that influence these outcomes.MethodsPregnant women’s pregnancy outcomes were collected from the medical information system and through telephone follow-ups. The chi-square test and logistic regression were used to analyze the factors influencing pregnancy outcomes.ResultsAmong 265 pregnant women diagnosed with fetal abnormalities, 190 chose to continue the pregnancy, while 75 chose to terminate it. Pregnant women with multiple fetal abnormalities (OR = 3.774, 95% CI [1.640–8.683]) were more likely to choose termination of pregnancy (TOP), and pregnant women who were advised to terminate their pregnancy or make a careful choice were more likely to terminate the pregnancy (OR = 41.113, 95% CI [11.028–153.267]).ConclusionThe number of organs involved in fetal abnormalities and treatment recommendations were identified as the primary factors influencing pregnancy outcomes. Improving awareness of maternal health care during pregnancy, early pregnancy screening technology, and a multidisciplinary diagnosis and treatment approach are of great significance in assisting pregnant women in making informed decisions and improving fetal prognosis. creator: Jing Ruan creator: Xuemei Zhong creator: Jiaxuan Mai creator: Cuifen Liu creator: Huiyang Ding uri: https://doi.org/10.7717/peerj.17284 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ruan et al. title: Application of prohexadione-calcium priming affects Brassica napus L. seedlings by regulating morph-physiological characteristics under salt stress link: https://peerj.com/articles/17312 last-modified: 2024-04-26 description: Salinity stress imposes severe constraints on plant growth and development. Here, we explored the impacts of prohexadione-calcium (Pro-Ca) on rapeseed growth under salt stress. We designed a randomized block design pot experiment using two rapeseed varieties, ‘Huayouza 158R’ and ‘Huayouza 62’. We conducted six treatments, S0: non-primed + 0 mM NaCl, Pro-Ca+S0: Pro-Ca primed + 0 mM NaCl, S100: non-primed + 100 mM NaCl, Pro-Ca+S100: Pro-Ca primed + 100 mM NaCl, S150: non-primed + 150 mM NaCl, Pro-Ca+S150: Pro-Ca primed + 150 mM NaCl. The morphophysiological characteristics, and osmoregulatory and antioxidant activities were compared for primed and non-primed varieties. Our data analysis showed that salt stress induced morph-physiological traits and significantly reduced the antioxidant enzyme activities in both rapeseed varieties. The Pro-Ca primed treatment significantly improved seedlings, root, and shoot morphological traits and accumulated more dry matter biomass under salt stress. Compared to Huayouza 158R, Huayouza 62 performed better with the Pro-Ca primed treatment. The Pro-Ca primed treatment significantly enhanced chlorophyll content, net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and actual photochemical quantum efficiency (ФPSII). Furthermore, the Pro-Ca primed treatment also improved ascorbic acid (ASA) content, superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) activity, and stimulated the accumulation of soluble proteins. These findings strongly suggested that the Pro-Ca primed treatment may effectively counteract the negative impacts of salinity stress by regulating the morph-physiological and antioxidant traits. creator: Peng Deng creator: Aaqil Khan creator: Hang Zhou creator: Xutong Lu creator: Huiming Zhao creator: Youwei Du creator: Yaxin Wang creator: Naijie Feng creator: Dianfeng Zheng uri: https://doi.org/10.7717/peerj.17312 license: https://creativecommons.org/licenses/by-nc/4.0 rights: © 2024 Deng et al. title: Exosomes from uterine fluid promote capacitation of human sperm link: https://peerj.com/articles/16875 last-modified: 2024-04-25 description: BackgroundExtracellular vesicles (EVs) are membrane-bound vesicles containing various proteins, lipids, and nucleic acids. EVs are found in many body fluids, such as blood and urine. The release of EVs can facilitate intercellular communication through fusion with the plasma membrane or endocytosis into the recipient cell or through internalization of the contents. Recent studies have reported that EVs isolated from human endometrial epithelial cells (EECs) promote sperm fertilization ability. EVs from uterine flushing fluid more closely resemble the physiological condition of the uterus. However, it is unclear whether EVs derived directly from uterine flushing fluid have the same effect on sperm. This study aimed to research the effect of EVs from uterine flushing fluid on sperm.MethodsEVs were isolated from the uterine flushing fluid. The presence of EVs was confirmed by nanoparticle tracking analysis (NTA), Western blot, and transmission electron microscopy (TEM). EVs were incubated with human sperm for 2 h and 4 h. The effects of EVs on sperm were evaluated by analyzing acrosome reaction, sperm motility, and reactive oxygen species (ROS).ResultsThe EVs fractions isolated from the uterine fluid were observed in cup-shaped vesicles of different sizes by TEM. All isolated vesicles contained similar numbers of vesicles in the expected size range (30–200 nm) by NTA. CD9 and CD63 were detected in EVs by western blot. Comparing the motility of the two groups incubated sperm motility significantly differed at 4 h. The acrosome reactions were promoted by incubating with EVs significantly. ROS were increased in sperm incubated with EVs.ConclusionOur results showed EVs present in the uterine fluid. Acrosome reactions and ROS levels increased in human sperm incubated with EVs. EVs from uterine fluid can promote the capacitation of human sperm. The increased capacitation after sperm interaction with EVs suggests a possible physiological effect during the transit of the uterus. creator: Renbin Deng creator: Zhao Wu creator: Chaoyong He creator: Chuncheng Lu creator: Danpeng He creator: Xi Li creator: Zhenling Duan creator: Hui Zhao uri: https://doi.org/10.7717/peerj.16875 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Deng et al. title: Natrix natrix after dark: citizen science sheds light on the common grass snake’s nightlife link: https://peerj.com/articles/17168 last-modified: 2024-04-25 description: Activity patterns in animals are often species-specific, and can be generally categorized as diurnal, crepuscular, or nocturnal. Understanding these patterns provides insight into ecological adaptations and behaviors. The common grass snake (Natrix natrix), one of the most common and widespread European snake species, is traditionally considered diurnal, with scarce evidence of its crepuscular and nocturnal activity. We aimed to document the distribution, environmental conditions, and potential phenotype associations of nighttime activity in N. natrix. We used citizen science data from iNaturalist (1992–2022), Observation.org (2012–2022), together with personal field observations (2010–2023) to collect 127 crepuscular and nocturnal activity records. Most observations occurred between May and August, coinciding with the peak activity period of grass snakes across their distribution range. Statistical analyses revealed no significant difference in mean daily temperatures between crepuscular and nocturnal observations. However, striped individuals displayed nocturnal activity at higher temperatures, consistent with their distribution in warmer regions, but failed to register any difference when tested on a geographic subsample, that accounted for sympatry of the phenotypes. Surprisingly, we found no significant impact of moon presence or moonlight on nighttime activity or age class, contrary to expectations based on other snake species’ responses. While our study reveals that nocturnal activity in the common grass snake is geographically widespread, further research is warranted to understand its drivers and ecological implications. This study highlights the value of citizen science platforms for biological and ecological research, offering unparalleled spatial and temporal coverage by their users. In conclusion, our work extends the knowledge of nocturnal behavior in N. natrix and underlines the critical role of citizen science in discovering behavioral aspects of common and widespread species. creator: Petronel Spaseni creator: Tiberiu C. Sahlean creator: Iulian Gherghel creator: Ștefan R. Zamfirescu creator: Ionuț C. Petreanu creator: Raluca Melenciuc creator: Cristina F. Alistar creator: Viorel D. Gavril creator: Alexandru Strugariu uri: https://doi.org/10.7717/peerj.17168 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Spaseni et al. title: Carbapenemase genes in clinical and environmental isolates of Acinetobacter spp. from Quito, Ecuador link: https://peerj.com/articles/17199 last-modified: 2024-04-25 description: Carbapenem-resistant Acinetobacter spp. is associated with nosocomial infections in intensive care unit patients, resulting in high mortality. Although Acinetobacter spp. represent a serious public health problem worldwide, there are a few studies related to the presence of carbapenemases in health care facilities and other environmental settings in Ecuador. The main aim of this study was to characterize the carbapenem-resistant Acinetobacter spp. isolates obtained from four hospitals (52) and from five rivers (27) close to Quito. We used the disc diffusion and EDTA sinergy tests to determine the antimicrobial susceptibility and the production of metallo β-lactamases, respectively. We carried out a multiplex PCR of gyrB gene and the sequencing of partial rpoB gene to bacterial species identification. We performed molecular screening of nine carbapenem-resistant genes (blaSPM, blaSIM, blaGIM, blaGES, blaOXA-23, blaOXA-24, blaOXA-51, blaOXA-58, and blaOXA-143) by multiplex PCR, followed by identification using sequencing of blaOXA genes. Our findings showed that carbapenem-resistant A. baumannii were the main species found in health care facilities and rivers. Most of the clinical isolates came from respiratory tract samples and harbored blaOXA-23, blaOXA-366, blaOXA-72, blaOXA-65, blaOXA-70, and blaOXA-143-like genes. The river isolates harbored only the blaOXA-51 and probably blaOXA-259 genes. We concluded that the most predominant type of carbapenem genes among isolates were both blaOXA-23 and blaOXA-65 among A. baumannii clinical isolates. creator: Nicole Sotomayor creator: José Eduardo Villacis creator: Noela Burneo creator: Jorge Reyes creator: Sonia Zapata creator: Rosa de los Ángeles Bayas-Rea uri: https://doi.org/10.7717/peerj.17199 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Sotomayor et al.