title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=406 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: CmHem, a hemolin-like gene identified from Cnaphalocrocis medinalis, involved in metamorphosis and baculovirus infection link: https://peerj.com/articles/16225 last-modified: 2023-10-04 description: BackgroundAs a member of the immunoglobulin superfamily, hemolins play a vital role in insect development and defense against pathogens. However, the innate immune response of hemolin to baculovirus infection varies among different insects.Methods and resultsIn this study, the hemolin-like gene from a Crambidae insect, Cnaphalocrocis medinalis, CmHem was cloned, and its role in insect development and baculovirus infection was analyzed. A 1,528 bp contig as potential hemolin-like gene of C. medinalis was reassembled from the transcriptome. Further, the complete hemolin sequence of C. medinalis (CmHem) was cloned and sequenced. The cDNA of CmHem was 1,515 bp in length and encoded 408 amino acids. The deduced amino acid of CmHem has relatively low identities (41.9–62.3%) to various insect hemolins. However, it contains four Ig domains similarity to other insect hemolins. The expression level of CmHem was the highest in eggs, followed by pupae and adults, and maintained a low expression level at larval stage. The synthesized siRNAs were injected into mature larvae, and the CmHem transcription decreased by 51.7%. Moreover, the abdominal somites of larvae became straightened, could not pupate normally, and then died. Infection with a baculovirus, C. medinalis granulovirus (CnmeGV), the expression levels of CmHem in the midgut and fat body of C. medinalis significantly increased at 12 and 24 h, respectively, and then soon returned to normal levels.ConclusionsOur results suggested that hemolin may be related to the metamorphosis of C. medinalis. Exposure to baculovirus induced the phased expression of hemolin gene in the midgut and fat body of C. medinalis, indicated that hemolin involved in the immune recognition of Crambidae insects to baculovirus. creator: Guangjie Han creator: Chuanming Li creator: Nan Zhang creator: Qin Liu creator: Lixin Huang creator: Yang Xia creator: Jian Xu uri: https://doi.org/10.7717/peerj.16225 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Han et al. title: Maize ZmHSP90 plays a role in acclimation to salt stress link: https://peerj.com/articles/15819 last-modified: 2023-10-03 description: BackgroundMaize is sensitive to salt stress, especially during the germination and seedling stages.MethodsWe conducted germination experiments on 60 maize materials under salt stress, and screened out the most salt-tolerant and salt-sensitive varieties based on germination indicators. Afterwards, transcriptome analysis was performed to screen for key regulators in the plumule and flag leaf at the germination and seedling stages, respectively. Following that, transgenic tobacco was developed to expose the roles and mechanisms of the candidate genes, enabling a deeper investigation of their functions.ResultsOut of the 60 inbred lines of maize, “975-12” exhibits the highest level of salt tolerance, while “GEMS64” displays the lowest. The application of salt stress resulted in a significant increase in the levels of antioxidant enzymes in both “975-12” and “GEMS64”. ABA signal transduction and jasmonic acid pathways were the pathways that mainly affected by salt stress. In addition, a significant finding has been made indicating that when exposed to high levels of salt stress, the expression of ZmHSP90 in ‘975-12’ increased while in ‘GEMS64’ decreased. Furthermore, in tobacco plants overexpressing ZmHSP90, there was an increase in antioxidant enzyme activity associated with salt tolerance. ZmHSP90 enhanced the expression levels of NtSOS1, NtHKT1, and NtNHX1 as compared to those in the salt treatment, causing the maintenance of Na+ and K+ homeostasis, suggesting that high expression of ZmHSP90 was conducive to regulate Na+ transporters to maintain K+/Na+ balanced in tobacco. creator: Xinyan Yu creator: Yanxin Zhao creator: Yun Wang creator: Zhiqing Zou creator: Fenghai Li uri: https://doi.org/10.7717/peerj.15819 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Yu et al. title: The complete mitochondrial genome and gene rearrangements in a gall wasp species, Dryocosmus liui (Hymenoptera: Cynipoidea: Cynipidae) link: https://peerj.com/articles/15865 last-modified: 2023-10-03 description: Mitochondrial genomes (mitogenomes) have been widely used in comparative and evolutionary genomics, molecular evolution, phylogenetics, and population genetics, but very limited information is available for the family Cynipidae. In this report, we describe the mitogenome of Dryocosmus liui Pang, Su et Zhu, providing the first complete mitogenomic data for a cynipid gall wasp species. The mitogenome of D. liui is 16,819 bp in length, and contains the typical set of 37 genes. Two control regions were detected, with the second being a perfect inverted repeat of the major portion of the first. Gene rearrangements were found in transfer RNA (tRNA) genes, protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes, compared with the putative ancestral mitogenome. Similar to two other Cynipidae species with mitogenome data available, D. liui has a novel tRNA gene cluster trnL1–trnI–trnL2–trnW–trnM–trnQ between nad1 and nad2. Phylogenetic analysis based on sequences of PCGs and rRNA genes with D. liui included obtained topologies identical to previous studies supporting the a relationship of (Cynipoidea , (Platygastroidea, Proctotrupoidea)) within the monophyletic Proctotrupomorpha and (Cynipidae, Figitidae), Ibaliidae) within the Cynipoidea. creator: Cheng-Yuan Su creator: Dao-Hong Zhu creator: Yoshihisa Abe creator: Tatsuya Ide creator: Zhiwei Liu uri: https://doi.org/10.7717/peerj.15865 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Su et al. title: An acoustic-based method for locating maternity colonies of rare woodland bats link: https://peerj.com/articles/15951 last-modified: 2023-10-03 description: Locating colonies of rare bats can be a time consuming process, as it is often difficult to know where to focus survey effort. However, identifying peaks of bat activity via acoustic monitoring may provide insights into whether a colony is locally present, and help screen out sites with low potential. Using a triage approach, we developed a survey methodology for locating colonies of the woodland-specialist barbastelle bat (Barbastella barbastellus). We investigated whether woodland occupancy by a colony could be predicted by acoustic data, and assessed the influence of survey effort (number of acoustic detectors deployed) on detectability. The methodology was then trialled in citizen science surveys of 77 woodlands, with follow-up radio-tracking surveys by specialists being used to confirm presence or absence. Using Receiver Operating Characteristic (ROC) curve analysis, we found that a threshold of four barbastelle passes recorded by at least one detector within one hour of sunset optimised the balance between the true- and false-positive rates. Subsequently, we found that a minimum survey effort of one detector per 6.25 hectares of woodland was needed to ensure a colony would be detected using this threshold, based on a survey sensitivity of 90%. Radio-tracking surveys in a subset of the woodlands, identified as having a high probability of being occupied by a colony based on acoustic monitoring, confirmed the presence of five previously unknown barbastelle maternity colonies. These results demonstrate that a triage system, in which high probability woodland sites are identified based on acoustic survey data, can be used to prioritise sites for future specialist surveys and conservation action. creator: Kieran D. O’Malley creator: Henry Schofield creator: Patrick G.R. Wright creator: Daniel Hargreaves creator: Tom Kitching creator: Marina Bollo Palacios creator: Fiona Mathews uri: https://doi.org/10.7717/peerj.15951 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 O’Malley et al. title: Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project link: https://peerj.com/articles/15978 last-modified: 2023-10-03 description: Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as “microbial gardening”. In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change. creator: Manuel Ochoa-Sánchez creator: Eliana Paola Acuña Gomez creator: Lia Ramírez-Fenández creator: Luis E. Eguiarte creator: Valeria Souza uri: https://doi.org/10.7717/peerj.15978 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Ochoa-Sánchez et al. title: High LYRM4-AS1 predicts poor prognosis in patients with glioma and correlates with immune infiltration link: https://peerj.com/articles/16104 last-modified: 2023-10-03 description: BackgroundMany researches proved that non-coding RNAs are important in glioma development. We screened the differentially expressed genes through The Cancer Genome Atlas (TCGA) database and identified the molecule LYRM4-AS1 associated with prognosis. As a lncRNA, the expression level and role of LYRM4-AS1 in glioma are inconclusive. Therefore, we attempted to assess the clinical significance, expression and related mechanisms of LYRM4-AS1 in glioma by employing cell experiments and an integrative in silico methodology.MethodsRNA-seq data were obtained from UCSC XENA and TCGA datasets. The Gene Expression Omnibus (GEO) database was used to download glioma-related expression profile data. The LYRM4-AS1 expression level was evaluated. Survival curves were constructed by the Kaplan–Meier method. Cox regression analysis was used to analyze independent variables. Patients were divided into high and low expression group base on the median LYRM4-AS1 expression value in glioma tissues. The DESeq2 R package was used to identify differentially expressed genes (DEGs) between two different expression LYRM4-AS1 groups. Gene set enrichment analysis (GSEA) was conducted. Next, the single-sample Gene Set Enrichment Analysis (ssGSEA) was done to quantify the immune infiltration of immune cells in glioma tissues. Gene expression profiles for glioma tumor tissues were used to quantify the relative enrichment score for each immune cell. Spearman correlation analysis was used to analyze the correlation between LYRM4-AS1 and biomarkers of immune cells as well as immune checkpoints in glioma. Finally, assays for cell apoptosis, cell viability and wound healing were conducted to evaluate the function on U87 MG and U251 cells after knocking down LYRM4-AS1.ResultsWe found that LYRM4-AS1 was upregulated and related to the grade and malignancy of glioma. Survival analyses showed that high expression LYRM4-AS1 patients had poor clinical outcomes (P < 0.01). Cox regression analyses demonstrated that LYRM4-AS1 was an independent risk factor for overall survival (OS) in glioma (HR: 274 1.836; CI [1.278–2.639]; P = 0.001). Enrichment and immune infiltration analysis showed interferon signaling and cytokine-cytokine receptor interaction enriched in the LYRM4-AS1 high-expression phenotype, and LYRM4-AS1 showed significantly positively related to immune infiltration as well as immune checkpoints (P < 0.01). The knockdown of LYRM4-AS1 in U87 MG and U251 cells can inhibit migration and proliferation of cells (P < 0.05).ConclusionsThese findings indicated that the increased LYRM4-AS1 may be useful for the diagnosis and prognosis of glioma and might participate in the immune infiltration. creator: Hai yue Wang creator: Ying Xie creator: Hongzhen Du creator: Bin Luo creator: Zengning Li uri: https://doi.org/10.7717/peerj.16104 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Wang et al. title: Characterization of macroalgal-associated microbial communities from shallow to mesophotic depths at Manawai, Papahānaumokuākea Marine National Monument, Hawai‘i link: https://peerj.com/articles/16114 last-modified: 2023-10-03 description: The Papahānaumokuākea Marine National Monument, Hawai‘i, is one of the most isolated and protected archipelagos in the world, making it a natural laboratory to examine macroalgal-microbial diversity because of limited direct anthropogenic impacts. We collected the most abundant macroalgae from nine sites ranging from shallow subtidal (1.5 m) to mesophotic (75 m) depths around Manawai (Pearl and Hermes Atoll). We characterized the macroalgal bacterial communities via high-throughput amplicon sequencing and compared the influence of host phylum, species, site, and depth on these relationships at a single atoll. Ochrophyta species had the lowest bacterial diversity compared to Chlorophyta and Rhodophyta. Site and/or depth may influence the microbial community structure associated with Microdictyon setchellianum, indicating a possible disconnect of these microbial communities among habitats. Chondria tumulosa, a cryptogenic species with invasive traits, differed in associated microbiota compared to the native Laurencia galtsoffii, an alga from the same family collected at the same site and depth. While there was overlap of bacterial communities across sites for some algal species, the majority had minimal macroalgal-microbial community connectivity across Manawai. This mesophotic system, therefore, did not appear to be refugia for shallow water coral reefs at microscopic scales. Additional studies are required to identify other significant influences on microbial community variation. creator: Gabrielle M. Kuba creator: Heather L. Spalding creator: Kristina M. Hill-Spanik creator: Taylor M. Williams creator: Monica O. Paiano creator: Alison R. Sherwood creator: Brian B. Hauk creator: Randall K. Kosaki creator: Heather Fullerton uri: https://doi.org/10.7717/peerj.16114 license: https://creativecommons.org/publicdomain/zero/1.0/ rights: title: Identification and validation of hub genes involved in foam cell formation and atherosclerosis development via bioinformatics link: https://peerj.com/articles/16122 last-modified: 2023-10-03 description: BackgroundFoam cells play crucial roles in all phases of atherosclerosis. However, until now, the specific mechanisms by which these foam cells contribute to atherosclerosis remain unclear. We aimed to identify novel foam cell biomarkers and interventional targets for atherosclerosis, characterizing their potential mechanisms in the progression of atherosclerosis.MethodsMicroarray data of atherosclerosis and foam cells were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expression genes (DEGs) were screened using the “LIMMA” package in R software. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Ontology (GO) annotation were both carried out. Hub genes were found in Cytoscape after a protein-protein interaction (PPI) enrichment analysis was carried out. Validation of important genes in the GSE41571 dataset, cellular assays, and tissue samples.ResultsA total of 407 DEGs in atherosclerosis and 219 DEGs in foam cells were identified, and the DEGs in atherosclerosis were mainly involved in cell proliferation and differentiation. CSF1R and PLAUR were identified as common hub genes and validated in GSE41571. In addition, we also found that the expression of CSF1R and PLAUR gradually increased with the accumulation of lipids and disease progression in cell and tissue experiments.ConclusionCSF1R and PLAUR are key hub genes of foam cells and may play an important role in the biological process of atherosclerosis. These results advance our understanding of the mechanism behind atherosclerosis and potential therapeutic targets for future development. creator: Da Teng creator: Hongping Chen creator: Wenjuan Jia creator: Qingmiao Ren creator: Xiaoning Ding creator: Lihui Zhang creator: Lei Gong creator: Hua Wang creator: Lin Zhong creator: Jun Yang uri: https://doi.org/10.7717/peerj.16122 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Teng et al. title: Effect of body mass index on soft tissues in adolescents with skeletal class I and normal facial height link: https://peerj.com/articles/16196 last-modified: 2023-10-03 description: BackgroundThe evaluation of soft tissues in patients undergoing orthodontic treatment plays a critical role in diagnosis and treatment planning. This study aims to evaluate the effect of body mass index (BMI) on facial soft tissues in skeletal Class I patients with normal vertical growth.MethodsThe study included 72 patients with a normal vertical growth pattern (SN-GoGn 26–38°) and skeletal Class I (ANB 2‒4°) malocclusion. According to their BMI (kg/m2) values, the patients were divided into three groups of 24 individuals each: underweight (>5th percentile) (13 females, 11 males; mean age, 11.58 ± 1.95 years), normal weight (5‒85th percentile) (12 females, 12 males; mean age, 11.54 ± 1.95 years), overweight (85‒95th percentile) (12 females, 12 males; mean age, 11.62 ± 2.01 years). Soft tissue thickness and height measurements were made on lateral cephalometric radiographs.ResultsIn all soft tissue thickness measurements, except for the nasion, the overweight weight group had higher values. In comparing the underweight and normal weight groups, statistically significant differences were found in the thickness measurements at the nasion and gnathion (p < 0.05). The differences in thickness measurements at the glabella, labiale superius, stomion, labiale inferius, pogonion, gnathion, and menton are statistically significant between the underweight and overweight groups (p < 0.005). Comparing the normal and overweight groups revealed statistically significant differences the thickness measurements at the glabella, labiale superius, stomion, pogonion and menton (p < 0.05). creator: Nurver Karsli creator: Esra Tuhan Kutlu uri: https://doi.org/10.7717/peerj.16196 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Karsli and Tuhan Kutlu title: Clinician motivational interviewing skills in ‘simulated’ and ‘real-life’ consultations differ and show predictive validity for ‘real life’ client change talk under differing integrity thresholds link: https://peerj.com/articles/14634 last-modified: 2023-10-02 description: BackgroundAccurate and reliable assessment of clinician integrity in the delivery of empirically supported treatments is critical to effective research and training interventions. Assessment of clinician integrity can be performed through recording simulated (SI) or real-life (RL) consultations, yet research examining the equivalence of these data is in its infancy. To explore the strength of integrity assessment between SI and RL samples in Motivational Interviewing (MI) consultations, this article examines whether Motivational Interviewing Treatment Integrity (MITI) assessments differ between SI and RL consultations and reviews the predictive validity of SI and RL MI skills categorisations for RL client response language.MethodsThis study first compared MITI coding obtained in SI and RL consultations for 36 veterinary clinicians. Multilevel models of 10 MITI behaviour counts and four MITI global scores were run using MLwiN 3.02 to assess if a significant difference existed between SI and RL MITI data, with consultation within clinician within cohort (A and B) as nested random effects. Second, we investigated the effect of SI and RL MI skills groupings on rate of RL client response talk using three multivariable regression models. Two Poisson regression models, with random intercepts for farm and veterinarian and offset for number of minutes of the recordings, were estimated in the statistical software R using the package glmmTMB for the two response variables Change Talk and Sustain Talk. A logistic regression model, with the same random intercepts, with the response variable Proportion Change Talk was also estimated using the same package.ResultsVeterinary clinicians were less MI consistent in RL consultations, evidenced through significantly lower global MITI Cultivating Change Talk (p < 0.001), Partnership (p < 0.001) and Empathy (p = 0.003) measures. Despite lower objective MI skills groupings in RL consultations, ranking order of veterinary clinicians by MI skills was similar between contexts. The predictive validity of SI and RL MI skills groupings for RL client Change Talk was therefore similar, with significantly more RL client Change Talk associated with veterinarians categorised in the highest grouping (‘moderate’) in both SI (p = 0.01) and RL (p = 0.02) compared to untrained veterinarians in each respective context.ConclusionsFindings suggest SI and RL data may not be interchangeable. Whilst both data offer useful insights for specific research and training purposes, differing contextual MI skills thresholds may offer a more equitable assessment of clinician RL client-facing MI integrity. Further research is needed to explore the applicability of these findings across health contexts. creator: Alison Bard creator: Lars Forsberg creator: Hans Wickström creator: Ulf Emanuelson creator: Kristen Reyher creator: Catarina Svensson uri: https://doi.org/10.7717/peerj.14634 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Bard et al.