title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=313 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Genome-wide identification and characterization of the AP2/ERF gene family in loblolly pine (Pinus taeda L.) link: https://peerj.com/articles/17388 last-modified: 2024-05-21 description: The loblolly pine (Pinus taeda L.) is one of the most profitable forest species worldwide owing to its quick growth, high wood yields, and strong adaptability. The AP2/ERF gene family plays a widespread role in the physiological processes of plant defense responses and the biosynthesis of metabolites. Nevertheless, there are no reports on this gene family in loblolly pine (P. taeda). In this study, a total of 303 members of the AP2/ERF gene family were identified. Through multiple sequence alignment and phylogenetic analysis, they were classified into four subfamilies, including AP2 (34), RAV (17), ERF (251), and Soloist (1). An analysis of the conservation domains, conserved motifs, and gene structure revealed that every PtAP2/ERF transcription factor (TF) had at least one AP2 domain. While evolutionary conservation was displayed within the same subfamilies, the distribution of conserved domains, conserved motifs, and gene architectures varied between subfamilies. Cis-element analysis revealed abundant light-responsive elements, phytohormone-responsive elements, and stress-responsive elements in the promoter of the PtAP2/ERF genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of potential target genes showed that the AP2/ERF gene family might play a critical role in plant growth and development, the response to environmental stresses, and metabolite biosynthesis. Utilizing quantitative real-time PCR (qRT-PCR), we examined the expression patterns of 10 randomly selected genes from Group IX after 6 h of treatments with mechanical injury, ethephon (Eth), and methyl jasmonate (MeJA). The AP2/ERF gene family in the loblolly pine was systematically analyzed for the first time in this study, offering a theoretical basis for exploring the functions and applications of AP2/ERF genes. creator: Peiqi Ye creator: Xiaoliang Che creator: Yang Liu creator: Ming Zeng creator: Wenbing Guo creator: Yongbin Long creator: Tianyi Liu creator: Zhe Wang uri: https://doi.org/10.7717/peerj.17388 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Ye et al. title: Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network link: https://peerj.com/articles/17396 last-modified: 2024-05-21 description: Deciphering the targets of microRNAs (miRNAs) in plants is crucial for comprehending their function and the variation in phenotype that they cause. As the highly cell-specific nature of miRNA regulation, recent computational approaches usually utilize expression data to identify the most physiologically relevant targets. Although these methods are effective, they typically require a large sample size and high-depth sequencing to detect potential miRNA-target pairs, thereby limiting their applicability in improving plant breeding. In this study, we propose a novel miRNA-target prediction framework named kmerPMTF (k-mer-based prediction framework for plant miRNA-target). Our framework effectively extracts the latent semantic embeddings of sequences by utilizing k-mer splitting and a deep self-supervised neural network. We construct multiple similarity networks based on k-mer embeddings and employ graph convolutional networks to derive deep representations of miRNAs and targets and calculate the probabilities of potential associations. We evaluated the performance of kmerPMTF on four typical plant datasets: Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, and Prunus persica. The results demonstrate its ability to achieve AUPRC values of 84.9%, 91.0%, 80.1%, and 82.1% in 5-fold cross-validation, respectively. Compared with several state-of-the-art existing methods, our framework achieves better performance on threshold-independent evaluation metrics. Overall, our study provides an efficient and simplified methodology for identifying plant miRNA-target associations, which will contribute to a deeper comprehension of miRNA regulatory mechanisms in plants. creator: Weihan Zhang creator: Ping Zhang creator: Weicheng Sun creator: Jinsheng Xu creator: Liao Liao creator: Yunpeng Cao creator: Yuepeng Han uri: https://doi.org/10.7717/peerj.17396 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: CircCamsap1 is dispensable for male fertility in mice link: https://peerj.com/articles/17399 last-modified: 2024-05-21 description: BackgroundCircular RNAs (circRNAs) are a large class of RNAs present in mammals. Among these, circCamsap1 is a well-acknowledged circRNA with significant implications, particularly in the development and progression of diverse tumors. However, the potential consequences of circCamsap1 depletion in vivo on male reproduction are yet to be thoroughly investigated.MethodsThe presence of circCamsap1 in the mouse testes was confirmed, and gene expression analysis was performed using reverse transcription quantitative polymerase chain reaction. CircCamsap1 knockout mice were generated utilizing the CRISPR/Cas9 system. Phenotypic analysis of both the testes and epididymis was conducted using histological and immunofluorescence staining. Additionally, fertility and sperm motility were assessed.ResultsHere, we successfully established a circCamsap1 knockout mouse model without affecting the expression of parental gene. Surprisingly, male mice lacking circCamsap1 (circCamsap1−/−) exhibited normal fertility, with no discernible differences in testicular and epididymal histology, spermatogenesis, sperm counts or sperm motility compared to circCamsap1+/+ mice. These findings suggest that circCamsap1 may not play an essential role in physiological spermatogenesis. Nonetheless, this result also underscores the complexity of circRNA function in male reproductive biology. Therefore, further research is necessary to elucidate the precise roles of other circRNAs in regulating male fertility. creator: Shu Zhang creator: Haojie Li creator: Wei Jiang creator: Xia Chen creator: Han Zhou creator: Chang Wang creator: Hao Kong creator: Yichao Shi creator: Xiaodan Shi uri: https://doi.org/10.7717/peerj.17399 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Zhang et al. title: No benefit of higher protein dosing in critically ill patients: a systematic review and meta-analysis of randomized controlled trials link: https://peerj.com/articles/17433 last-modified: 2024-05-21 description: PurposeThe optimal range of protein dosage and effect of high-dose protein on critically ill patients remain controversial. We conducted a meta-analysis to compare higher and lower doses of protein supplementation for nutritional support in critically ill patients.MethodsWe searched the PubMed, Embase, Scopus, and Cochrane Library databases for randomized controlled trials that compared higher (≥1.2 g/kg per day) versus lower (<1.2 g/kg per day) doses of protein supplementation among critically ill adult patients. This search spanned from the inception of relevant databases to November 20, 2023. Our primary endpoint of interest was overall mortality, while secondary endpoints included length of stay in the intensive care unit, length of hospital stay, duration of mechanical ventilation, and incidence of acute kidney injury.ResultsSeventeen studies including 2,965 critically ill patients were included in our meta-analysis. The pooled analyses showed no significant difference in overall mortality (RR 1.03, 95%CI [0.92–1.15], P = 0.65, I2 = 0%), length of intensive care unit stay (MD 0.19, 95%CI [−0.67 to 1.04], P = 0.66, I2 = 25%), length of hospital stay (MD 0.73, 95%CI [−1.59 to 3.04], P = 0.54, I2 = 27%), duration of mechanical ventilation (MD −0.14, 95%CI [−0.83 to 0.54], P = 0.68, I2 = 8%), and incidence of acute kidney injury (RR 1.11, 95%CI [0.87–1.41], P = 0.38, I2 = 0%) between critically ill patients receiving higher or lower doses of protein supplementation.ConclusionsFor critically ill patients, the protein supplementation dose had no significant effect on clinical outcomes, including overall mortality, length of intensive care unit and hospital stay, duration of mechanical ventilation, and incidence of acute kidney injury. creator: Yonggen Qin creator: Jian Huang creator: Xiaofeng Ping creator: Hui Zheng creator: Kai Zhang creator: Xiaoya Xu creator: Jiuqing Yu uri: https://doi.org/10.7717/peerj.17433 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Qin et al. title: Exploring the influence of self-identification on perceptual judgments of physical and social causality link: https://peerj.com/articles/17449 last-modified: 2024-05-21 description: People tend to overestimate the causal contribution of the self to the observed outcome in various situations, a cognitive bias known as the ‘illusion of control.’ This study delves into whether this cognitive bias impacts causality judgments in animations depicting physical and social causal interactions. In two experiments, participants were instructed to associate themselves and a hypothetical stranger identity with two geometrical shapes (a circle and a square). Subsequently, they viewed animations portraying these shapes assuming the roles of agent and patient in causal interactions. Within one block, the shape related to the self served as the agent, while the shape associated with the stranger played the role of the patient. Conversely, in the other block, the identity-role association was reversed. We posited that the perception of the self as a causal agent might influence explicit judgments of physical and social causality. Experiment 1 demonstrated that physical causality ratings were solely shaped by kinematic cues. In Experiment 2, emphasising social causality, the dominance of kinematic parameters was confirmed. Therefore, contrary to the hypothesis anticipating diminished causality ratings with specific identity-role associations, results indicated negligible impact of our manipulation. The study contributes to understanding the interplay between kinematic and non-kinematic cues in human causal reasoning. It suggests that explicit judgments of causality in simple animations primarily rely on low-level kinematic cues, with the cognitive bias of overestimating the self’s contribution playing a negligible role. creator: Michele Vicovaro creator: Francesca Squadrelli Saraceno creator: Mario Dalmaso uri: https://doi.org/10.7717/peerj.17449 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Vicovaro et al. title: Alteration of RNA m6A methylation mediates aberrant RNA binding protein expression and alternative splicing in condyloma acuminatum link: https://peerj.com/articles/17376 last-modified: 2024-05-20 description: BackgroundCondyloma acuminatum (CA) is caused by low-risk human papillomavirus, and is characterized by high recurrence after treatment. The RNA modification N6-methyladenosine (m6A) plays an important role during diverse viral infections, including high-risk HPV infection in cervical cancer. However, it is unclear whether low-risk HPV infection changes the RNA m6A methylation in CA.MethodsHigh-throughputm6A-sequencing was performed to profile the transcriptome-wide mRNA modifications of CA tissues infected by LR-HPVs and the paired normal tissues from CA patients. We further investigated the regulation of alternative splicing by RNA binding proteins (RBPs) with altered m6A modification and constructed a regulatory network among these RBPs, regulated alternative splicing events (RASEs) and regulated alternative splicing genes (RASGs) in CA.ResultsThe results show that the m6A level in CA tissues differed from that in the paired controls. Furthermore, cell cycle- and cell adhesion- associated genes with m6A modification were differentially expressed in CA tissues compared to the paired controls. In particular, seven RNA binding protein genes with specific m6A methylated sites, showed a higher or lower expression at the mRNA level in CA tissues than in the paired normal tissues. In addition, these differentially expressed RNA binding protein genes would regulate the alternative splicing pattern of apoptotic process genes in CA tissue.ConclusionsOur study reveals a sophisticated m6A modification profile in CA tissue that affects the response of host cells to HPV infection, and provides cues for the further exploration of the roles of m6A and the development of a novel treatment strategy for CA. creator: Xiaoyan Liu creator: Bo Xie creator: Su Wang creator: Yinhua Wu creator: Yu Zhang creator: Liming Ruan uri: https://doi.org/10.7717/peerj.17376 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Liu et al. title: PTX3 mediates PI3K/AKT/mTOR signaling to downregulate apoptosis and autophagy to attenuate myocardial injury in sepsis link: https://peerj.com/articles/17263 last-modified: 2024-05-20 description: BackgroundThis study aimed to investigate the effect and mechanism of Pentraxin 3 (PTX3) on myocardial injury in sepsis.MethodsThirty male C57BL/6 mice were randomly assigned to Groups A, B, or C. Mice in Groups A and B were injected with unloaded lentivirus, while mice in Group C were injected with lentivirus encoding PTX3 overexpression. Seven days after injection, septic myocardial injury mouse models were constructed following intraperitoneal injection with LPS in Groups B and C, and mice in Group A were intraperitoneally injected with normal saline. Cardiac function was examined using echocardiography; pathological variation of myocardial cells was measured through HE staining, transmission electron microscopy, and TUNEL staining; and Western blot was used to measure the expression of PI3K/AKT/mTOR pathway-related, autophagy-related, and apoptosis-related proteins in mice myocardial cells.ResultsPTX3 significantly improved cardiac function and structure in sepsis-stricken mice, and PTX3 alleviated cardiac damage caused by sepsis. PTX3 reduced the relative protein expression of p-PI3K, p-AKT, mTOR, LC3I/II, Beclin, ATG5, Bax, Caspase-3, and Caspase-9 in septic mouse cardiomyocytes and increased the relative protein expression of Bcl-2.ConclusionPTX3 can attenuate myocardial injury in sepsis due to the down-regulation of apoptosis and autophagy induced by the PI3K/AKT/mTOR pathway. creator: Na Cui creator: Zhi Chen creator: Zhanbiao Yu creator: Xiaowei Lv creator: Zhenjie Hu uri: https://doi.org/10.7717/peerj.17263 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Cui et al. title: Comparative genomics reveals high genetic similarity among strains of Salmonella enterica serovar Infantis isolated from multiple sources in Brazil link: https://peerj.com/articles/17306 last-modified: 2024-05-20 description: BackgroundSalmonella enterica serovar Infantis (Salmonella Infantis) is a zoonotic, ubiquitous and foodborne pathogen of worldwide distribution. Despite Brazil’s relevance as a major meat exporter, few studies were conducted to characterize strains of this serovar by genomic analyses in this country. Therefore, this study aimed to assess the diversity of 80 Salmonella Infantis strains isolated from veterinary, food and human sources in Brazil between 2013 and 2018 by comparative genomic analyses. Additional genomes of non-Brazilian countries (n = 18) were included for comparison purposes in some analyses.MethodsAnalyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries.ResultswgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes. Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to biological processes, molecular functions, and cellular components were detected among Brazilian and non-Brazilian genomes.ConclusionThe results presented using different genomic approaches emphasized the significant genomic similarity among Brazilian Salmonella Infantis genomes analyzed, suggesting wide distribution of closely related genotypes among diverse sources in Brazil. The data generated contributed to novel information regarding the genomic diversity of Brazilian and non-Brazilian Salmonella Infantis in comparison. The different genetically related subtypes of Salmonella Infantis from Brazil can either occur exclusively within the country, or also in other countries, suggesting that some exportation of the Brazilian genotypes may have already occurred. creator: Felipe P. Vilela creator: Andrei G. Felice creator: Amanda A. Seribelli creator: Dália P. Rodrigues creator: Siomar C. Soares creator: Marc W. Allard creator: Juliana P. Falcão uri: https://doi.org/10.7717/peerj.17306 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Vilela et al. title: Temperature-driven dynamics: unraveling the impact of climate change on cryptic species interactions within the Litoditis marina complex link: https://peerj.com/articles/17324 last-modified: 2024-05-20 description: Anthropogenic climate change and the associated increase in sea temperatures are projected to greatly impact marine ecosystems. Temperature variation can influence the interactions between species, leading to cascading effects on the abundance, diversity and composition of communities. Such changes in community structure can have consequences on ecosystem stability, processes and the services it provides. Therefore, it is important to better understand the role of species interactions in the development of communities and how they are influenced by environmental factors like temperature. The coexistence of closely related cryptic species, with significant biological and ecological differences, makes this even more complex. This study investigated the effect of temperature on species growth and both intra- and interspecific interactions of three species within the free-living nematode Litoditis marina complex. To achieve this, closed microcosm experiments were conducted on the L. marina species Pm I, Pm III and Pm IV in monoculture and combined cultures at two temperature treatments of 15 °C and 20 °C. A population model was constructed to elucidate and quantify the effects of intra- and interspecific interactions on nematode populations. The relative competitive abilities of the investigated species were quantified using the Modern Coexistence Theory (MCT) framework. Temperature had strong and disparate effects on the population growth of the distinct L. marina species. This indicates temperature could play an important role in the distribution of these cryptic species. Both competitive and facilitative interactions were observed in the experiments. Temperature affected both the type and the strength of the species interactions, suggesting a change in temperature could impact the coexistence of these closely related species, alter community dynamics and consequently affect ecosystem processes and services. creator: Anna-Maria Vafeiadou creator: Kevin Geldhof creator: Wissam Barhdadi creator: Jan M. Baetens creator: Bernard De Baets creator: Tom Moens creator: Aisling J. Daly uri: https://doi.org/10.7717/peerj.17324 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Vafeiadou et al. title: A novel chaperone-effector-immunity system identified in uropathogenic Escherichia coli UMN026 link: https://peerj.com/articles/17336 last-modified: 2024-05-20 description: BackgroundUrinary tract infections (UTIs) are very common worldwide. According to their symptomatology, these infections are classified as pyelonephritis, cystitis, or asymptomatic bacteriuria (AB). Approximately 75–95% of UTIs are caused by uropathogenic Escherichia coli (UPEC), which is an extraintestinal bacterium that possesses virulence factors for bacterial adherence and invasion in the urinary tract. In addition, UPEC possesses type 6 secretion systems (T6SS) as virulence mechanisms that can participate in bacterial competition and in bacterial pathogenicity. UPEC UMN026 carries three genes, namely, ECUMN_0231, ECUMN_0232, and ECUMN_0233, which encode three uncharacterized proteins related to the T6SS that are conserved in strains from phylogroups B2 and D and have been proposed as biomarkers of UTIs.AimTo analyze the frequency of the ECUMN_0231, ECUMN_0232, ECUMN_0233, and vgrG genes in UTI isolates, as well as their expression in Luria Bertani (LB) medium and urine; to determine whether these genes are related to UTI symptoms or bacterial competence and to identify functional domains on the putative proteins.MethodsThe frequency of the ECUMN and vgrG genes in 99 clinical isolates from UPEC was determined by endpoint PCR. The relationship between gene presence and UTI symptomatology was determined using the chi2 test, with p < 0.05 considered to indicate statistical significance. The expression of the three ECUMN genes and vgrG was analyzed by RT-PCR. The antibacterial activity of strain UMN026 was determined by bacterial competence assays. The identification of functional domains and the docking were performed using bioinformatic tools.ResultsThe ECUMN genes are conserved in 33.3% of clinical isolates from patients with symptomatic and asymptomatic UTIs and have no relationship with UTI symptomatology. Of the ECUMN+ isolates, only five (15.15%, 5/33) had the three ECUMN and vgrG genes. These genes were expressed in LB broth and urine in UPEC UMN026 but not in all the clinical isolates. Strain UMN026 had antibacterial activity against UPEC clinical isolate 4014 (ECUMN−) and E. faecalis but not against isolate 4012 (ECUMN+). Bioinformatics analysis suggested that the ECUMN genes encode a chaperone/effector/immunity system.ConclusionsThe ECUMN genes are conserved in clinical isolates from symptomatic and asymptomatic patients and are not related to UTI symptoms. However, these genes encode a putative chaperone/effector/immunity system that seems to be involved in the antibacterial activity of strain UMN026. creator: América Casiano González creator: Arantxa Pacheco Villanueva creator: Natividad Castro-Alarcón creator: Julio Méndez creator: Ricardo Oropeza creator: Verónica I. Martínez-Santos uri: https://doi.org/10.7717/peerj.17336 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Casiano González et al.