title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=536 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Association between INHA gene polymorphisms and litter size in Hainan black goats link: https://peerj.com/articles/15381 last-modified: 2023-05-09 description: BackgroundThe inhibin alpha (INHA) gene is one of the important genes affecting the reproductive traits of animals. Hainan black goats are the main goat breed in Hainan Island (China), whose development is limited by low reproductive performance. However, the relationship between INHA gene and the reproductive performance of Hainan black goats is still unclear. Therefore, the purpose of this work was to explore the effect of INHA gene polymorphisms on the litter size of Hainan black goats.MethodsSingle nucleotide polymorphisms (SNPs) of INHA were detected, and the genetic parameters and haplotype frequency of these SNPs were calculated and association analysis was performed for these SNPs with the litter size. Finally, the SNP with significant correlations to litter size was analyzed by Bioinformatics tools.ResultsThe results showed that the litter size of individuals with the AC genotype at loci g.28317663A>C of INHA gene was significantly higher than those with the AA genotype. This SNP changed the amino acid sequence, which may affect the function of INHA protein by affecting its structure. Our results suggest that g.28317663A>C loci may serve as a potential molecular marker for improving the reproductive traits in Hainan black goats. creator: Zhengyu Bian creator: Kunpeng Li creator: Si Chen creator: Churiga Man creator: Fengyang Wang creator: Lianbin Li uri: https://doi.org/10.7717/peerj.15381 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Bian et al. title: The effects of the E3 ubiquitin–protein ligase UBR7 of Frankliniella occidentalis on the ability of insects to acquire and transmit TSWV link: https://peerj.com/articles/15385 last-modified: 2023-05-09 description: The interactions between plant viruses and insect vectors are very complex. In recent years, RNA sequencing data have been used to elucidate critical genes of Tomato spotted wilt ortho-tospovirus (TSWV) and Frankliniella occidentalis (F. occidentalis). However, very little is known about the essential genes involved in thrips acquisition and transmission of TSWV. Based on transcriptome data of F. occidentalis infected with TSWV, we verified the complete sequence of the E3 ubiquitin-protein ligase UBR7 gene (UBR7), which is closely related to virus transmission. Additionally, we found that UBR7 belongs to the E3 ubiquitin–protein ligase family that is highly expressed in adulthood in F. occidentalis. UBR7 could interfere with virus replication and thus affect the transmission efficiency of F. occidentalis. With low URB7 expression, TSWV transmission efficiency decreased, while TSWV acquisition efficiency was unaffected. Moreover, the direct interaction between UBR7 and the nucleocapsid (N) protein of TSWV was investigated through surface plasmon resonance and GST pull-down. In conclusion, we found that UBR7 is a crucial protein for TSWV transmission by F. occidentalis, as it directly interacts with TSWV N. This study provides a new direction for developing green pesticides targeting E3 ubiquitin to control TSWV and F. occidentalis. creator: Junxia Shi creator: Junxian Zhou creator: Fan Jiang creator: Zhihong Li creator: Shuifang Zhu uri: https://doi.org/10.7717/peerj.15385 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Shi et al. title: 1H NMR fecal metabolic phenotyping of periductal fibrosis- and cholangiocarcinoma-specific metabotypes defining perturbation in gut microbial-host co-metabolism link: https://peerj.com/articles/15386 last-modified: 2023-05-09 description: BackgroundThe liver fluke Opisthorchis viverrini (OV), which subsequently inhabits the biliary system and results in periductal fibrosis (PDF), is one of the primarily causes of cholangiocarcinoma (CCA), a bile duct cancer with an exceptionally high incidence in the northeast of Thailand and other Greater Mekong Subregion (GMS) countries. Insights in fecal metabolic changes associated with PDF and CCA are required for further molecular research related to gut health and potential diagnostic biological marker development.MethodsIn this study, nuclear magnetic resonance (NMR) metabolomics was applied for fecal metabolic phenotyping from 55 fecal water samples across different study groups including normal bile duct, PDF and CCA groups.ResultsBy using NMR spectroscopy-based metabolomics, fecal metabolic profiles of patients with CCA or PDF and of individuals with normal bile duct have been established with a total of 40 identified metabolites. Further multivariate statistical analysis and hierarchical clustering heat map have demonstrated the PDF- and CCA-specific metabotypes through various altered metabolite groups including amino acids, alcohols, amines, anaerobic glycolytic metabolites, fatty acids, microbial metabolites, sugar, TCA cycle intermediates, tryptophan catabolism substrates, and pyrimidine metabolites. Compared to the normal bile duct group, PDF individuals showed the significantly elevated relative concentrations of fecal ethanol, glycine, tyrosine, and N-acetylglucosamine whereas CCA patients exhibited the remarkable fecal metabolic changes that can be evident through the increased relative concentrations of fecal uracil, succinate, and 5-aminopentanoate. The prominent fecal metabolic alterations between CCA and PDF were displayed by the reduction of relative concentration of methanol observed in CCA. The metabolic alterations associated with PDF and CCA progression have been proposed with the involvement of various metabolic pathways including TCA cycle, ethanol biogenesis, hexamine pathway, methanol biogenesis, pyrimidine metabolism, and lysine metabolism. Among them, ethanol, methanol, and lysine metabolism strongly reflect the association of gut-microbial host metabolic crosstalk in PDF and/or CCA patients.ConclusionThe PDF- and CCA-associated metabotypes have been investigated displaying their distinct fecal metabolic patterns compared to that of normal bile duct group. Our study also demonstrated that the perturbation in co-metabolism of host and gut bacteria has been involved from the early step since OV infection to CCA tumorigenesis. creator: Rujikorn Treeriya creator: Phuc N. Ho creator: Attapol Titapun creator: Poramate Klanrit creator: Manida Suksawat creator: Thanaporn Kulthawatsiri creator: Suphasarang Sirirattanakul creator: Watcharin Loilome creator: Nisana Namwat creator: Arporn Wangwiwatsin creator: Nittaya Chamadol creator: Narong Khuntikeo creator: Jutarop Phetcharaburanin uri: https://doi.org/10.7717/peerj.15386 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Treeriya et al. title: LINC00106/RPS19BP1/p53 axis promotes the proliferation and migration of human prostate cancer cells link: https://peerj.com/articles/15232 last-modified: 2023-05-08 description: BackgroundProstate cancer (PCa) is among the most prevalent cancers in males with high biochemical recurrence risk. LINC00106 contributes to the carcinogenesis of Hepatocellular carcinoma (HCC). However, it is unclear how it affects PCa advancement. Here, we studied LINC00106’s effects on PCa cells’ ability to proliferate, invade, and metastasize.MethodsThe data of LINC00106 from The Cancer Genome Atlas (TCGA) in human PCa tissues were analyzed using TANRIC and survival analysis. In order to determine the expression levels of genes and proteins, we also performed reverse transcription-quantitative PCR and western blot analysis. The migration, invasion, colony formation, and proliferation (CCK-8) of PCa cells with LINC00106 knockdown were investigated. The impact of LINC00106 on cell proliferation and invasion was also analyzed in mice. LncRNA prediction software catRAPID omics v2.1 (catRAPID omics v2.0 (tartaglialab.com)) was used to predict proteins that might interact with LINC00106. The interactions were verified via RNA immunoprecipitation and RNA pull-down assays and finally, the interaction between LINC00106 and its target protein and the p53 signaling pathway was studied using a dual-luciferase reporter assay.ResultsIn PCa, LINC00106 was over-expressed in comparison to normal tissues, and it was linked to an unfavorableprognosis. In vitro and in vivo analyses showed that downregulating LINC00106 decreased PCa cells’ability to proliferate and migrate. A common regulatory axis generated by LINC00106 and RPS19BP1 prevents p53 activity.ConclusionOur experimental data indicate that LINC00106 functions as an oncogene in the onset of PCa, and the LINC00106/RPS19BP1/P53 axis canserve as a novel therapeutic target for PCa treatment. creator: Lingxiang Lu creator: Zhen Tian creator: Jicheng Lu creator: Minjun Jiang creator: Jianchun Chen creator: Shuai Guo creator: Yuhua Huang uri: https://doi.org/10.7717/peerj.15232 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Lu et al. title: Analysing the effectiveness of Twitter as an equitable community communication tool for international conferences link: https://peerj.com/articles/15270 last-modified: 2023-05-08 description: Scientific conferences increasingly include online aspects. Some are moving to be entirely virtual whilst others are adopting hybrid models in which there are both in-person and virtual elements. This development of opportunities for people to attend conferences virtually has the potential to both reduce their environmental impact and to make access to them more equitable. An issue with virtual conference participation that has been raised, however, is that there is a reduction in informal communication between attendees. This is an important deficit as informal contacts play a significant role in both knowledge transmission and professional network development. One forum where some informal communication around conferences does occur is Twitter, with participation there being encouraged by some conferences. It is not clear, however, how effective Twitter is as a community communication tool in terms of equitable participation amongst conference attendees. To investigate this, we looked at Twitter usage surrounding four international conferences between 2010 and 2021. It was found that engagement with conference hashtags increased steadily over time, peaking in 2019. Users represented 9% of conference attendees and were primarily located in Europe and North America, communicating primarily in English (97% of tweets). Hub nodes within the interaction network were also primarily located in these regions. East Asia had fewer users than would be expected based on neuroscience publication numbers from that region. What users there were in East Asia were engaged with less than were users in other regions. It was found that the overall interaction network showed a rich-club structure, where users with more connections tend to interact more with others with similar connection numbers. Finally, it was found that users in Europe and North America tend to communicate with other users in their own regions whereas users in the rest of the world direct their interactions out of their region. These results suggest that although conference-related Twitter use has been successful to some degree in opening up access, there are some notable limitations in its usage that may mirror aspects of inequality inherent to in-person conferences. How to build equitable informal communication networks around virtual conferences remains a challenging question that requires further discussion. creator: Niall W. Duncan creator: Russell Shean uri: https://doi.org/10.7717/peerj.15270 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Duncan and Shean title: Effects of defoliation and nitrogen on carbon dioxide (CO2) emissions and microbial communities in soils of cherry tree orchards link: https://peerj.com/articles/15276 last-modified: 2023-05-08 description: BackgroundIn farmland, microbes in soils are affected by exogenous carbon, nitrogen, and soil depth and are responsible for soil organic carbon (SOC) mineralization. The cherry industry has been evolving rapidly in northwest China and emerged as a new source of income for local farmers to overcome poverty. Accordingly, it is highly imperative to probe the effect of defoliation and nitrogen addition on carbon dioxide (CO2) emissions and microbial communities in soils of dryland cherry orchards.MethodsCO2 emissions and microbial communities were determined in soil samples at three depths, including 0–10 cm, 10–30 cm, and 30–60 cm, from a 15-year-old rain-fed cherry orchard. The samples were respectively incubated with or without 1% defoliation under three input levels of nitrogen (0 mg kg−1, 90 mg kg−1, and 135 mg kg−1) at 25°C in the dark for 80 days.ResultsDefoliation and nitrogen addition affected CO2 emissions and microbial communities and increased microbial biomass carbon (MBC), the activity of soil catalase, alkaline phosphatase, and cellulase in soils of the dryland cherry orchard. The culture with defoliation significantly promoted CO2 emissions in soils at the three depths mainly by increasing the MBC, catalase, alkaline phosphatase, and cellulase activities, resulted in positive priming index. Nitrogen addition elevated the MBC and changed soil enzymes and reduced CO2 emissions in soils at the three depths. Moreover, the priming index was higher in deep soils than in top and middle soils under the condition of defoliation and nitrogen addition. No significant differences were observed in the soil bacterial diversity (Chao1, Shannon, and Simpson) among all treatments. Meanwhile, the relative abundance of Proteobacteria was markedly increased and that of Acidobacteria was substantially diminished in soils at the three depths by defoliation and nitrogen addition. The results sustained that defoliation and nitrogen can regulate SOC dynamics by directly and indirectly affecting soil microbial activities and communities. As a result, the combination of defoliation return and nitrogen fertilization management is a promising strategy to increase SOC and promote soil quality in dryland cherry orchards. creator: Jing Wang creator: Yibo Wang creator: Ruifang Xue creator: Dandan Wang creator: Wenhui Nan uri: https://doi.org/10.7717/peerj.15276 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Wang et al. title: EIF4A3 serves as a prognostic and immunosuppressive microenvironment factor and inhibits cell apoptosis in bladder cancer link: https://peerj.com/articles/15309 last-modified: 2023-05-08 description: EIF4A3 (Eukaryotic translation initiation factor 4A3 (EIF4A3) was recently recognized as an oncogene; however, its role in BLCA (bladder cancer) remains unclear. We explored EIF4A3 expression and its prognostic value in BLCA in public datasets, including the TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus). Thereafter, the association between EIF4A3 expression and the infiltration of immune cells and immune-checkpoint expression was determined using TIMER2 (Tumor Immune Estimation Resource 2) tool. Additionally, the impact of EIF4A3 on cellular proliferation and apoptosis events in BLCA cell lines was determined by siRNA technology. In this study, EIF4A3 was found to be significantly upregulated in BLCA, upregulated expression of EIF4A3 was related to poor prognosis, advanced histologic grade, subtype, pathological stage, white race, and poor primary therapy outcome. The immune infiltration analysis revealed that EIF4A3 expression was negatively associated with CD8+ and CD4+ T cells and positively with myeloid-derived suppressor cells, macrophage M2, cancer-associated fibroblasts, and Treg cells. Moreover, EIF4A3 was coexpressed with PD-L1 (programmed cell death 1-ligand 1) and its expression was higher in patients responding to anti-PD-L1 therapy. EIF4A3 knockdown significantly inhibited proliferation and promoted apoptosis in 5,637 and T24 cells. In summary, BLCA patients with elevated EIF4A3 expression had an unfavorable prognosis and immunosuppressive microenvironment, and EIF4A3 may facilitate BLCA progression by promoting cell proliferation and inhibiting apoptosis. Furthermore, our study suggests that EIF4A3 is a potential biomarker and therapeutic target for BLCA. creator: Bing Hu creator: Ru Chen creator: Ming Jiang creator: Situ Xiong creator: Xiaoqiang Liu creator: Bin Fu uri: https://doi.org/10.7717/peerj.15309 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Hu et al. title: Identifying liver metastasis-related hub genes in breast cancer and characterizing SPARCL1 as a potential prognostic biomarker link: https://peerj.com/articles/15311 last-modified: 2023-05-08 description: BackgroundThe liver is the third most common metastatic site for advanced breast cancer (BC), and liver metastases predict poor prognoses. However, the characteristic biomarkers of BC liver metastases and the biological role of secreted protein acidic and rich in cysteine-like 1 (SPARCL1) in BC remain unclear. The present study aimed to identify potential biomarkers for liver metastasis of BC and to investigate the effect of SPARCL1 on BC.MethodsThe publicly available GSE124648 dataset was used to identify differentially expressed genes (DEGs) between BC and liver metastases. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to annotate these DEGs and understand the biological functions in which they are involved. A protein–protein interaction (PPI) network was constructed to identify metastasis-related hub genes and further validated in a second independent dataset (GSE58708). Clinicopathological correlation of hub gene expression in patients with BC was determined. Gene set enrichment analysis (GSEA) was performed to explore DEG-related signaling pathways. SPARCL1 expression in BC tissues and cell lines was verified by RT-qPCR. Further in vitro experiments were performed to investigate the biological functions of SPARCL1 in BC cells.ResultsWe identified 332 liver metastasis-related DEGs from GSE124648 and 30 hub genes, including SPARCL1, from the PPI network. GO and KEGG enrichment analyses of liver-metastasis-related DEGs revealed several enriched terms associated with the extracellular matrix and pathways in cancer. Clinicopathological correlation analysis of SPARCL1 revealed that its expression in BC was associated with age, TNM stage, estrogen receptor status, progesterone receptor status, histological type, molecular type, and living status of patients. GSEA results suggested that low SPARCL1 expression in BC was related to the cell cycle, DNA replication, oxidative phosphorylation, and homologous recombination. Lower expression levels of SPARCL1 were detected in BC tissues compared to adjacent tissues. The in vitro experiments showed that SPARCL1 knockdown significantly increased the proliferation and migration of BC cells, whereas the proliferation and migration were suppressed after elevating the expression of SPARCL1.ConclusionWe identified SPARCL1 as a tumor suppressor in BC, which shows potential as a target for BC and liver metastasis therapy and diagnosis. creator: Mingkuan Chen creator: Wenfang Zheng creator: Lin Fang uri: https://doi.org/10.7717/peerj.15311 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen et al. title: The effect of combined dietary supplementation of herbal additives on carcass traits, meat quality, immunity and cecal microbiota composition in Hungarian white geese link: https://peerj.com/articles/15316 last-modified: 2023-05-08 description: The present study was performed to investigate the effects of dietary supplementation with herbal additives on meat quality, slaughter performance and the cecal microbial community in Hungarian white geese. A total of 60 newborn geese were assigned equally into the control group (CON) and the herbal complex supplemented group (HS). The dietary supplementations consisted of Compound Herbal Additive A (CHAA) including Pulsatilla, Gentian and Rhizoma coptidis, and Compound Herbal Additive B (CHAB) containing Codonopsis pilosula, Atractylodes, Poria cocos and Licorice. The geese in the HS group received a basal diet supplemented with 0.2% CHAA from day 0 to day 42 at the postnatal stage. Then from day 43 to day 70, the geese in HS group were provide a basal diet with 0.15% CHAB. The geese in the CON group were only provided with the basal diet. The results showed that the slaughter rate (SR), half chamber rates (HCR), eviscerated rate (ER) and breast muscle rate (BMR) in the HS group tended to increase slightly compared with the CON group (ns). In addition, the shear force, filtration rate and pH value of breast muscle and thigh muscle in the HS group were slightly enhanced compared to the CON group (ns). Significant increased levels in carbohydrate content, fat content and energy (P < 0.01) and significant decreased levels in cholesterol content (P < 0.01) were observed in the muscle of the HS group. The total amino acid (Glu, Lys, Thr and Asp) content in the muscle increased in HS group than in the CON group (P < 0.01). Dietary herb supplementations significantly increased the levels of IgG in serum (P < 0.05) on day 43 and higher levels of IgM, IgA and IgG (P < 0.01) were also observed in the HS group on day 70. Furthermore, 16S rRNA sequencing results indicated that herbal additives increased the growth of beneficial bacteria and inhibited the proliferation of harmful bacteria in the geese caecum. Altogether, these results offer crucial insights into the potential benefits of incorporating CHAA and CHAB into the diets of Hungarian white goose. The findings indicate that such supplementations could significantly improve meat quality, regulate the immune system and shape the intestinal microbiota composition. creator: Guilin Fu creator: Yuxuan Zhou creator: Yupu Song creator: Chang Liu creator: Manjie Hu creator: Qiuyu Xie creator: Jingbo Wang creator: Yuxin Zhang creator: Yumeng Shi creator: Shuhao Chen creator: Jingtao Hu creator: Yongfeng Sun uri: https://doi.org/10.7717/peerj.15316 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Fu et al. title: Cardiac sensitivity to rewards in cognitively inflexible nonclinical participants link: https://peerj.com/articles/15318 last-modified: 2023-05-08 description: BackgroundIn psychopathologies characterized by compulsive decision-making, core impairments include cognitive inflexibility and excessive sensitivity to rewards. It has been posited that traits shared by nonclinical individuals and psychiatric patients could help explain the pathogenesis of compulsive decision-making.MethodsTo investigate whether cognitive inflexibility predisposes nonclinical individuals to poor choices and hyper-reactivity to reward, we recruited people with high and low scores for cognitive persistence and used the Iowa Gambling Task to assess decision-making and cardiac reactivity to monetary gains/losses.ResultsAs is frequently observed in psychophysiological research, the data indicated discrepancies among self-reports, behavior, and physiology. Cognitive inflexibility was not related to worse performance; however, monetary gains, in line with the literature, prompted marked cardiac accelerations. Consistent with our research goal, only inflexible participants showed large cardiac accelerations during the largest monetary wins.DiscussionTaken together, the data confirm an association between cognitive persistence and physiological reward sensitivity in a nonclinical population. The findings are in line with recent theories on the development of compulsive behaviors that consider cognitive inflexibility as a transdiagnostic impairment and predisposing factor for excessive reactivity to rewards, and might act both as a preexisting individual trait and drug-induced deficit. creator: José Luis Mata creator: Azahara Leonor Miranda Gálvez creator: Francisca López Torrecillas creator: Laura Miccoli uri: https://doi.org/10.7717/peerj.15318 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Mata et al.