title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=745 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Dissection of genetic architecture for tiller angle in rice (Oryza sativa. L) by multiple genome-wide association analyses link: https://peerj.com/articles/12674 last-modified: 2022-03-10 description: BackgroundThe rice plant architecture is determined by spatially and temporally domesticated tiller angle. The deeper insight into the genetic mechanism for rice plant architecture will allow more efficient light capture by increasing the planting density, reproducibility, and the ability to survive in a stressful environment.MethodsIn this study, a natural population of 795 genotypes further divided into japonica and indica subpopulations, was evaluated for tiller angle. A significant variation with a wide range was observed. Genome-wide association analysis was performed by the general linear model (GLM), and compressed mix linear model (cMLM) for three populations to disclose the genomic associations. The population principal components and kinship matrix in 1,000 permutations were used to remove the false positives. The candidate genes were evaluated for their functional annotations and specific molecular pathways. The sequencing-based haplotype analysis was further performed to reveal the functional variation among candidate genomic regions.ResultsAs a result, 37 significant QTLs with 93 annotated loci were identified. Among the loci, a known tiller angle controlling locus TAC1 was also identified. The introduction of the sequence pooling technique was observed fruitful to screen the 12 significant QTLs with 22 annotated loci. For ten of these loci, the functional variations were identified by haplotype analysis. These results were not only providing a better understanding of the genetic bases of rice plant architecture but also provide significant information for future breeding programs. creator: Muhammad Abdul Rehman Rashid creator: Rana Muhammad Atif creator: Yan Zhao creator: Farrukh Azeem creator: Hafiz Ghulam Muhu-Din Ahmed creator: Yinghua Pan creator: Danting Li creator: Yong Zhao creator: Zhanying Zhang creator: Hongliang Zhang creator: Jinjie Li creator: Zichao Li uri: https://doi.org/10.7717/peerj.12674 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Rashid et al. title: Genotypic variation in root architectural traits under contrasting phosphorus levels in Mediterranean and Indian origin lentil genotypes link: https://peerj.com/articles/12766 last-modified: 2022-03-10 description: The development of phosphorus-efficient crop cultivars boosts productivity while lowering eutrophication in the environment. It is feasible to improve the efficiency of phosphorus (P) absorption in lentils by enhancing phosphorus absorption through root architectural traits. The root architectural traits of 110 diverse lentil genotypes of Indian and Mediterranean origin were assessed, and the relationships between traits were investigated. In a hydroponics experiment, the lentil lines were examined at the seedling stage under two conditions: adequate P supply and deficient P supply. The Pearson correlation coefficients between root architectural traits and genetic diversity among lentil lines were assessed. To estimate variance components, a model (fixed factor) was used. In this experiment, both phosphorus (P) and genotype were fixed variables. Our lentil lines showed significant genetic variability and considerable genetic diversity for all traits under both treatments. The TRL (total root length) and PRL (primary root length) showed strong positive associations with all other characteristics excluding root average diameter (RAD) in both P treatments. In both P treatments, the RAD revealed a negative significant association with Total Root Tips (TRT), as well as total root volume (TRV) and total root forks (TRF) in the deficit conditions of P. Total root volume (TRV), total surface area (TSA), and total root tips had higher coefficient variance values. The first two principal components represented 67.88% and 66.19% of the overall variance in the adequate and deficit P treatments respectively. The Shannon-Weaver diversity index (H′) revealed that RAD, PRL, and TSA had more variability than TRT and TRF under both treatments. According to the Comprehensive Phosphorus Efficiency Measure (CPEM), the best five highly efficient genotypes are PLL 18-09, PLS 18-01, PLL 18-25, PLS 18-23, and PLL 18-07, while IG112131, P560206, IG334, L11-231, and PLS18-67 are highly inefficient genotypes. The above contrasting diverse lentil genotypes can be utilized to produce P-efficient lentil cultivars. The lentil germplasm with potentially favorable root traits can be suggested to evaluated for other abiotic stress to use them in crop improvement programme. The scientific breakthroughs in root trait phenotyping have improved the chances of establishing trait–allele relationships. As a result, genotype-to-phenotype connections can be predicted and verified with exceptional accuracy, making it easier to find and incorporate favourable nutrition-related genes/QTLs in to breeding programme. creator: Muraleedhar Aski creator: Reena Mehra creator: Gyan Prakash Mishra creator: Dharmendra Singh creator: Prachi Yadav creator: Neha Rai creator: Venkata Ravi Prakash Reddy creator: Arun Kumar MB creator: Renu Pandey creator: Madan Pal Singh creator: Gayacharan creator: Ruchi Bansal creator: Kuldeep Tripathi creator: Sripada M. Udupa creator: Shiv Kumar creator: Ashutosh Sarker creator: Harsh Kumar Dikshit uri: https://doi.org/10.7717/peerj.12766 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Aski et al. title: A versatile isothermal amplification assay for the detection of leptospires from various sample types link: https://peerj.com/articles/12850 last-modified: 2022-03-10 description: BackgroundLeptospirosis is a zoonotic disease caused by bacteria of the genus Leptospira that affects both humans and animals worldwide. Early detection of the pathogen in humans is crucial for early intervention and control of the progression of the disease to a severe state. It is also vitally important to be able to detect the presence of the pathogen in carrier animals to control the spread of the disease from the environment. Here we developed a simple and rapid loop-mediated isothermal amplification (LAMP) assay targeting the leptospiral secY gene.ResultsSeveral reaction conditions of the LAMP reaction were optimized to ensure efficient amplification of the target DNA. The sensitivity of the developed LAMP assay obtained using a pure Leptospira culture was 2 × 104 copies of genomic DNA per reaction (equivalent to 0.1 ng) for a 40-minute reaction time. No cross-reactions were observed in the LAMP reaction against a series of non-leptospiral bacteria, indicating a specific reaction. The applicability of the LAMP assay was demonstrated on human blood and urine specimens collected from suspected leptospirosis patients and rat kidney specimens collected from suspected leptospirosis outbreak areas and high-risk areas. The developed LAMP assay demonstrated a higher detection rate for leptospiral DNA compared with the polymerase chain reaction (PCR) assay, possibly due to the presence of inhibitory substances, especially in rat kidney specimens, to which the PCR method is more susceptible. The present findings also highlight the importance of urine sample collection from patients for routine monitoring of the disease.ConclusionsIn short, the developed LAMP assay can serve as a feasible alternative tool for the diagnosis of leptospirosis and be used for epidemiological and environmental surveillance of the disease, considering its robustness, rapidity, sensitivity, and specificity, as demonstrated in this study. creator: Shuhaidah Othman creator: Pui-Yuei Lee creator: Jia-Yong Lam creator: Noraini Philip creator: Nurul Natasya Azhari creator: Norliza Bahtiar Affendy creator: Siti Norbaya Masri creator: Vasantha Kumari Neela creator: Farah Shafawati Mohd-Taib creator: Hui-Yee Chee uri: https://doi.org/10.7717/peerj.12850 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Othman et al. title: Expression of IER3 in hepatocellular carcinoma: clinicopathology, prognosis, and potential regulatory pathways link: https://peerj.com/articles/12944 last-modified: 2022-03-10 description: BackgroundImmediate early response 3 (IER3) is correlated to the prognosis of several cancers, but the precise mechanisms underlying the regulation by IER3 of the occurrence and development of hepatocellular carcinoma (HCC) remain unknown.MethodsThe expression level of IER3 was examined by using in-house immunohistochemistry (IHC), public gene chip, and public RNA-sequencing (RNA-seq). The standardized mean difference (SMD) was calculated to compare the expression levels of IER3 between HCC patients and controls. The summary receiver operating characteristics (sROC) was plotted to comprehensively understand the discriminatory capability of IER3 between HCC and non-HCC group. The Kaplan–Meier curves and the combined hazard ratios (HRs) were used to determine the prognostic value of IER3 in HCC. Moreover, differentially expressed genes (DEGs) and co-expression genes (CEGs) were used to explored the molecular mechanisms of IER3 underlying HCC. hTFtarget was used to predict the transcription factors (TFs) of IER3. The binding site of TFs and the IER3 promoter region was forecasted using the JASPAR website. The relevant ChIP-seq data were used to determine whether TF peaks were present in the IER3 transcription initiation.ResultsA significantly increased expression of IER3 protein was found in HCC tissue relative to non-HCC tissue as detected by IHC (p < 0.001). Compared to 1,263 cases of non-HCC tissues, IER3 in 1483 cases of HCC tissues was upregulated (SMD = 0.42, 95% confidence interval [CI] [0.09–0.76]). The sROC showed that IER3 had a certain ability at differentiating HCC tissues (area under the curve (AUC) = 0.65, 95% CI [0.61–0.69]). Comprehensive analysis of the effect of IER3 on the prognosis of patients with HCC demonstrated that higher IER3 expression was associated with poor prognosis in HCC (HRs = 1.30, 95% CI [1.03–1.64]). Pathway enrichment analysis revealed that IER3-related genes were mostly enriched in the PI3K-Akt signaling pathway, cancer-related signaling pathways, the p53 signaling pathway, and other signaling pathways. Regulatory factor X5 (RFX5) was identified as a possible regulator of IER3-related TF.ConclusionIER3 may be a potential prognostic marker for HCC. The molecular mechanisms of IER3 in HCC warrant further study. creator: Fei-Yan He creator: Gang Chen creator: Rong-quan He creator: Zhi-Guang Huang creator: Jian-Di Li creator: Wei-Zi Wu creator: Ji-Tian Chen creator: Yu-Lu Tang creator: Dong-Ming Li creator: Shang-Ling Pan creator: Zhen-Bo Feng creator: Yi-wu Dang uri: https://doi.org/10.7717/peerj.12944 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 He et al. title: First observations of ovary regeneration in an amphipod, Ampelisca eschrichtii Krøyer, 1842 link: https://peerj.com/articles/12950 last-modified: 2022-03-10 description: BackgroundFemales of the gammaridean amphipod Ampelisca eschrichtii with signs of regenerating, previously atrophied ovaries were recovered from the northeastern shelf of Sakhalin Island (Okhotsk Sea, Russia). Ovarian regeneration was previously unknown for any amphipod species. A. eschrichtii have a predominantly 2-year life cycle (from embryo to adult death) and reproduce once between late winter or early spring at the age of 2 years. Occasionally, females survive to a third year. An adaptive value of extended survival among these females is likely to require that they are also reproductive.MethodsHistological sections from a second-year female with ovarian atrophy, a female with normal ovaries, a third-year female with ovarian regeneration, as well as testes of an immature and a sexually mature male were compared to determine the sources of cells of the germinal and somatic lines necessary for ovarian regeneration.ResultsOvarian regeneration in the third-year female began with the formation of a new germinal zone from germ cells preserved in the atrophied ovaries and eosinophilic cells of the previously starving second-year female. Eosinophilic cells form the mesodermal component of the germinal zone. A mass of these cells appeared in the second-year female that had atrophied ovaries and in large numbers on the intestine wall of the third-year female with regenerating ovaries. These eosinophilic cells appear to migrate into the regenerating ovaries.ConclusionsAll germ cells of the second-year female are not lost during ovarian atrophy and can be involved in subsequent ovarian regeneration. Eosinophilic cells involved in ovarian regeneration are of mesodermal origin. The eosinophilic cell morphologies are similar to those of quiescence cells (cells in a reversible state that do not divide but retain the ability to re-enter cell division and participate in regeneration). These histological data thus indicate that eosinophilic and germ cells of third-year females can participate in the regeneration of the ovaries to reproduce a second brood. The precursors of these third-year females (a small number the second-year females with an asynchronous [summer] breeding period and ovaries that have atrophied due to seasonal starvation) appear to possess sources of somatic and germ cells that are sufficient for ovarian regeneration and that may be adaptations to starvation stress. creator: Valentina B. Durkina creator: John W. Chapman creator: Natalia L. Demchenko uri: https://doi.org/10.7717/peerj.12950 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Durkina et al. title: Evaluation of the diagnostic and prognostic values of serum HSP90α in sepsis patients: a retrospective study link: https://peerj.com/articles/12997 last-modified: 2022-03-10 description: BackgroundSepsis is a serious syndrome that is caused by immune responses dysfunction and leads to high mortality. The abilities of heat shock protein 90α (HSP90α) in assessing the diagnosis and prognosis in patients with sepsis remain ill-defined to date. We conducted a study to reveal the possible clinical applications of HSP90α as biomarker for the diagnosis and prognosis in patients with sepsis.MethodsIn total, 150 patients of sepsis, 110 patients without sepsis admitted to ICU and 110 healthy subjects were involved in this study. The serum HSP90α contents, sequential organ failure assessment (SOFA) scores, procalcitonin (PCT), and short-term survival status of the participants were measured and compared. Logistic and linear regression models adjusting for potential confounders were used to examine the association of HSP90α with sepsis survival. Moreover, serum IL-1β, IL-18, MIP-3α, and ENA-78 were also determined. Finally, Spearman correlation analysis was employed to reveal a possible mechanism that HSP90α contributed to the short-term deaths.ResultsSerum HSP90α levels in sepsis patients were higher than those in ICU controls and healthy controls (P < 0.001), and even increased in patients who died within 28 days (P < 0.001). Logistic and linear regression models identified HSP90α was an independent risk factors for sepsis mortality. Receiver operating characteristic (ROC) analysis displayed that HSP90α had a considerable predictive performance for sepsis outcome, with an area under curve (AUC) value up to 0.79. Survival analysis demonstrated that the mortality of sepsis individuals at 28 days was positively associated with HSP90α levels, especially the levels of HSP90α were greater than 120 ng/mL (P < 0.001). Moreover, among sepsis patients, those who died had notably elevated cytokines, IL-1β, IL-18, and chemokines, MIP-3α, ENA-78, relative to survivors. Further correlation analysis demonstrated that there was a nominally positive correlation between HSP90α and IL-1β, IL-18, and MIP-3α.ConclusionHSP90α is of favorable clinical significance in sepsis diagnosis and prognosis, laying a foundation for future clinical applications. creator: Fuxing Li creator: Yulin Zhang creator: Bocheng Yu creator: Zihua Zhang creator: Yujuan Fan creator: Li Wang creator: Mingjing Cheng creator: Ping Yan creator: Weidong Zhao uri: https://doi.org/10.7717/peerj.12997 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Li et al. title: Effect of magnification factor by Galilean loupes on working posture of dental students in simulated clinical procedures: associations between direct and observational measurements link: https://peerj.com/articles/13021 last-modified: 2022-03-10 description: ObjectivesTo determine the effect of different levels of Galilean loupe magnification on working posture as measured by compliance with ergonomic posture positions, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back region during simulated clinical conditions.MethodsAn experimental laboratory study was performed in which the dependent variables were compliance with ergonomic posture requirements while performing simulated restorative procedures in Restorative Dentistry, angular deviation from the neutral position of the neck, and muscle activation in the neck and upper back. The independent variable was the level of Galilean loupe magnification, which was tested at four levels (naked eye, 2.5× magnification, 3.0× magnification, and 3.5× magnification). The cavity preparations and Class I composite resin restorations were performed on artificial first molars on a mannequin in a dental chair. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) was used for the postural analysis; as was an analysis of the angular deviation from the neutral position of the neck and surface electromyography. Working posture was recorded on video over the course of the procedure. Participants were filmed from three different angles. The Compliance Assessment of Dental Ergonomic Posture Requirements (CADEP) assessed compliance with ergonomic posture requirements. A locally produced posture assessment software analyzed angular deviation. Surface electromyography bilaterally assessed activation of the sternocleidomastoid, descending trapezius and ascending trapezius muscles. Two-factor analysis of variance (ANOVA) and either Tukey’s post-hoc test or the Games-Howell post-hoc test were performed (α = 0.05).ResultsDuring the cavity preparations and restorations, the use of Galilean loupes at all magnifications positively influenced working posture as measured by participants’ compliance with ergonomic posture positions (p < 0.01) and neck angulation (p < 0.01); the use of these loupes did not affect muscle activation in the regions evaluated (p > 0.05).ConclusionThe use of Galilean loupes had a positive effect on dental students’ working posture during the restoration procedures performed. creator: Júlia Margato Pazos creator: Simone Cecilio Hallak Regalo creator: Paulo de Vasconcelos creator: Juliana Alvares Duarte Bonini Campos creator: Patricia Petromilli Nordi Sasso Garcia uri: https://doi.org/10.7717/peerj.13021 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Pazos et al. title: Functional analysis of ARF1 from Cymbidium goeringii in IAA response during leaf development link: https://peerj.com/articles/13077 last-modified: 2022-03-10 description: BackgroundCymbidium is an economically important genus of flowering orchids cultivated in China because of showing graceful leaf shapes and elegant flower coloration. However, the deterioration of the ecological environment and the difficulty of conservation management have become increasing challenges for maintaining its germplasm resources. ARFs are critical transcription factors in the auxin signaling pathway and have been found to play pivotal roles in leaf growth and development in previous studies. However, their functions and mechanisms in Cymbidium goeringii remain to be clarified.MethodsThe sequence of the CgARF1 gene was analyzed by bioinformatics. The expression of this gene in different tissues and under IAA treatment was detected by quantitative real-time PCR analysis. The CgARF1 gene was overexpressed in wild-type Arabidopsis and Nicotiana benthamiana via the Agrobacterium infection method. Acetone-ethanol solvent extraction was applied for the determination of chlorophyll contents, and the contents of endogenous hormones were determined using the enzyme-linked immunosorbent assay technique.ResultsCgARF1 cloned from C. goeringii ‘Songmei’ was 2,049 bp in length and encoded 682 amino acids containing three typical domains: a B3 DNA binding domain, an Aux_resp domain and an AUX/IXX family domain. The expression pattern of CgARF1 in different tissues of C. goeringii showed that its expression was highest in the leaves and changed greatly under IAA treatment. Subcellular localization studies showed that the protein was mainly localized in the cell nucleus. CgARF1-overexpressing lines exhibited leaf senescence and a decreased chlorophyll content. Under IAA treatment, CgARF1 regulates the rooting length, rooting number and rooting rate from detached leaves. The levels of endogenous hormones in transgenic leaves were also significantly changed.ConclusionThese results indicated that CgARF1 overexpression is responsive to IAA treatment during leaf development. This study provides a foundation for future research on the function of the ARF gene family in C. goeringii. creator: Zihan Xu creator: Fangle Li creator: Meng Li creator: Yuanhao He creator: Yue Chen creator: Fengrong Hu uri: https://doi.org/10.7717/peerj.13077 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Xu et al. title: Effect of precipitation change on the photosynthetic performance of Phragmites australis under elevated temperature conditions link: https://peerj.com/articles/13087 last-modified: 2022-03-10 description: BackgroundAs a fundamental metabolism, leaf photosynthesis not only provides necessary energy for plant survival and growth but also plays an important role in global carbon fixation. However, photosynthesis is highly susceptible to environmental stresses and can be significantly influenced by future climate change.MethodsIn this study, we examined the photosynthetic responses of Phragmites australis (P. australis) to three precipitation treatments (control, decreased 30%, and increased 30%) under two thermal regimes (ambient temperature and +4 °C) in environment-controlled chambers.ResultsOur results showed that the net CO2 assimilation rate (Pn), maximal rate of Rubisco (Vcmax), maximal rate of ribulose-bisphosphate (RuBP) regeneration (Jmax) and chlorophyll (Chl) content were enhanced under increased precipitation condition, but were declined drastically under the condition of water deficit. The increased precipitation had no significant effect on malondialdehyde (MDA) content (p > 0.05), but water deficit drastically enhanced the MDA content by 10.1%. Meanwhile, a high temperature inhibited the positive effects of increased precipitation, aggravated the adverse effects of drought. The combination of high temperature and water deficit had more detrimental effect on P. australis than a single factor. Moreover, non-stomatal limitation caused by precipitation change played a major role in determining carbon assimilation rate. Under ambient temperature, Chl content had close relationship with Pn (R2 = 0.86, p < 0.01). Under high temperature, Pn was ralated to MDA content (R2 = 0.81, p < 0.01). High temperature disrupted the balance between Vcmax and Jmax (the ratio of Jmax to Vcmax decreased from 1.88 to 1.12) which resulted in a negative effect on the photosynthesis of P. australis. Furthermore, by the analysis of Chl fluorescence, we found that the xanthophyll cycle-mediated thermal dissipation played a major role in PSII photoprotection, resulting in no significant change on actual PSII quantum yield (ΦPSII) under both changing precipitation and high temperature conditions.ConclusionsOur results highlight the significant role of precipitation change in regulating the photosynthetic performance of P. australis under elevated temperature conditions, which may exacerbate the drought-induced primary productivity reduction of P. australis under future climate scenarios. creator: Linhong Teng creator: Hanyu Liu creator: Xiaonan Chu creator: Xiliang Song creator: Lianhui Shi uri: https://doi.org/10.7717/peerj.13087 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Teng et al. title: Feature screening for survival trait with application to TCGA high-dimensional genomic data link: https://peerj.com/articles/13098 last-modified: 2022-03-10 description: BackgroundIn high-dimensional survival genomic data, identifying cancer-related genes is a challenging and important subject in the field of bioinformatics. In recent years, many feature screening approaches for survival outcomes with high-dimensional survival genomic data have been developed; however, few studies have systematically compared these methods. The primary purpose of this article is to conduct a series of simulation studies for systematic comparison; the second purpose of this article is to use these feature screening methods to further establish a more accurate prediction model for patient survival based on the survival genomic datasets of The Cancer Genome Atlas (TCGA).ResultsSimulation studies prove that network-adjusted feature screening measurement performs well and outperforms existing popular univariate independent feature screening methods. In the application of real data, we show that the proposed network-adjusted feature screening approach leads to more accurate survival prediction than alternative methods that do not account for gene-gene dependency information. We also use TCGA clinical survival genetic data to identify biomarkers associated with clinical survival outcomes in patients with various cancers including esophageal, pancreatic, head and neck squamous cell, lung, and breast invasive carcinomas.ConclusionsThese applications reveal advantages of the new proposed network-adjusted feature selection method over alternative methods that do not consider gene-gene dependency information. We also identify cancer-related genes that are almost detected in the literature. As a result, the network-based screening method is reliable and credible. creator: Jie-Huei Wang creator: Cai-Rong Li creator: Po-Lin Hou uri: https://doi.org/10.7717/peerj.13098 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2022 Wang et al.