Genome-wide identification and evolution of the SAP gene family in sunflower (Helianthus annuus L.) and expression analysis under salt and drought stress
Stress-associated proteins (SAPs) are known to play an important role in plant responses to abiotic stresses. This study systematically identified members of the sunflower SAP gene family using sunflower genome data. The genes of the sunflower SAP gene family were analyzed using bioinformatic methods, and gene expression was assessed through fluorescence quantification (qRT-PCR) under salt and drought stress. A comprehensive analysis was also performed on the number, structure, collinearity, and phylogeny of seven Compositae species and eight other plant SAP gene families. The sunflower genome was found to have 27 SAP genes, distributed across 14 chromosomes. The evolutionary analysis revealed that the SAP family genes could be divided into three subgroups. Notably, the annuus variety exhibited amplification of the SAP gene for Group 3. Among the Compositae species, C. morifolium demonstrated the highest number of collinearity gene pairs and the closest distance on the phylogenetic tree, suggesting relative conservation in the evolutionary process. An analysis of gene structure revealed that Group 1 exhibited the most complex gene structure, while the majority of HaSAP genes in Group 2 and Group 3 lacked introns. The promoter analysis revealed the presence of cis-acting elements related to ABA, indicating their involvement in stress responses. The expression analysis indicated the potential involvement of 10 genes (HaSAP1, HaSAP3, HaSAP8, HaSAP10, HaSAP15, HaSAP16, HaSAP21, HaSAP22, HaSAP23, and HaSAP26) in sunflower salt tolerance. The expression of these 10 genes were then examined under salt and drought stress using qRT-PCR, and the tissue-specific expression patterns of these 10 genes were also analyzed. HaSAP1, HaSAP21, and HaSAP23 exhibited consistent expression patterns under both salt and drought stress, indicating these genes play a role in both salt tolerance and drought resistance in sunflower. The findings of this study highlight the significant contribution of the SAP gene family to salt tolerance and drought resistance in sunflower.
Zhang et al. (2024) Genome-wide identification and evolution of the SAP gene family in sunflower (Helianthus annuus L.) and expression analysis under salt and drought stress. PeerJ 12:e17808 https://doi.org/10.7717/peerj.17808
Are dietary factors associated with cardiometabolic risk factors in patients with non-alcoholic fatty liver disease?
Background Non-alcoholic fatty liver disease (NAFLD) is intricately linked with dietary patterns and metabolic homeostasis. Therefore, the present study focused to investigate the relation between dietary patterns and cardiometabolic risk factors related to fatty liver in NAFLD patients. Methods This cross-sectional study included 117 individuals whose body mass index (BMI) threshold of 25 or above diagnosed with NAFLD by magnetic resonance imaging. The hospital database was used to review the patients’ medical records such as lipid parameters, and fasting blood sugar. Anthropometric measurements and body composition were measured by researchers. Likewise, data from 24-h dietary recalls of individuals were collected to analyze their energy and nutrient intakes besides calculating dietary insulin index (DII), dietary insulin load (DIL), dietary glycemic index (DGI), and dietary glycemic load (DGL). Results Participants consuming diets with distinct levels of DII, DIL, DGI, and DGL exhibited variations in dietary energy and nutrient intake. Specifically, differences were noted in carbohydrate intake across quartiles of DII, DIL, DGI, and DGL, while fructose consumption showed variability in DGL quartiles (p ≤ 0.05). Moreover, sucrose intake demonstrated distinctions in both DII and DGL quartiles (p ≤ 0.05). No statistical difference was found in biochemical parameters and the fatty liver index among different levels of DII, DIL, DGI, and DGL (p > 0.05). After adjusting for potential confounders, participants with a higher DGI had four times greater odds of developing metabolic syndrome compared to those in the bottom quartile (OR, 4.32; 95% CI [1.42–13.11]). Conclusion This study provides initial evidence of the intricate association between dietary factors and NAFLD, emphasizing the necessity for further research including prospective designs with larger sample sizes, to garner additional insights.
Topal et al. (2024) Are dietary factors associated with cardiometabolic risk factors in patients with non-alcoholic fatty liver disease?. PeerJ 12:e17810 https://doi.org/10.7717/peerj.17810
Prevalence and metabolic risk factors of chronic kidney disease among a Mexican adult population: a cross-sectional study in primary healthcare medical units
Introduction The intricate relationship between obesity and chronic kidney disease (CKD) progression underscores a significant public health challenge. Obesity is strongly linked to the onset of several health conditions, including arterial hypertension (AHTN), metabolic syndrome, diabetes, dyslipidemia, and hyperuricemia. Understanding the connection between CKD and obesity is crucial for addressing their complex interplay in public health strategies. Objective This research aimed to determine the prevalence of CKD in a population with high obesity rates and evaluate the associated metabolic risk factors. Material and Methods In this cross-sectional study conducted from January 2017 to December 2019 we included 3,901 participants of both sexes aged ≥20 years who were selected from primary healthcare medical units of the Mexican Social Security Institute (IMSS) in Michoacan, Mexico. We measured the participants’ weight, height, systolic and diastolic blood pressure, glucose, creatinine, total cholesterol, triglycerides, HDL-c, LDL-c, and uric acid. We estimated the glomerular filtration rate using the Collaborative Chronic Kidney Disease Epidemiology (CKD-EPI) equation. Results Among the population studied, 50.6% were women and 49.4% were men, with a mean age of 49 years (range: 23–90). The prevalence of CKD was 21.9%. Factors significantly associated with an increased risk of CKD included age ≥60 years (OR = 11.70, 95% CI [9.83–15.93]), overweight (OR = 4.19, 95% CI [2.88–6.11]), obesity (OR = 13.31, 95% CI [11.12–15.93]), abdominal obesity (OR = 9.25, 95% CI [7.13–11.99]), AHTN (OR = 20.63, 95% CI [17.02–25.02]), impaired fasting glucose (IFG) (OR = 2.73, 95% CI [2.31–3.23]), type 2 diabetes (T2D) (OR = 14.30, 95% CI [11.14–18.37]), total cholesterol (TC) ≥200 mg/dL (OR = 6.04, 95% CI [5.11–7.14]), triglycerides (TG) ≥150 mg/dL (OR = 5.63, 95% CI 4.76-6.66), HDL-c <40 mg/dL (OR = 4.458, 95% CI [3.74–5.31]), LDL-c ≥130 mg/dL (OR = 6.06, 95% CI [5.12–7.18]), and serum uric acid levels ≥6 mg/dL in women and ≥7 mg/dL in men (OR = 8.18, 95% CI [6.92–9.68]), (p < 0.0001). These factors independently contribute to the development of CKD. Conclusions This study underscores the intricate relationship between obesity and CKD, revealing a high prevalence of CKD. Obesity, including overweight, abdominal obesity, AHTN, IFG, T2D, dyslipidemia, and hyperuricemia emerged as significant metabolic risk factors for CKD. Early identification of these risk factors is crucial for effective intervention strategies. Public health policies should integrate both pharmacological and non-pharmacological approaches to address obesity-related conditions and prevent kidney damage directly.
Alvarez Paredes et al. (2024) Prevalence and metabolic risk factors of chronic kidney disease among a Mexican adult population: a cross-sectional study in primary healthcare medical units. PeerJ 12:e17817 https://doi.org/10.7717/peerj.17817
Acute effects of voluntary isometric contractions at maximal shortening vs. ballistic stretching on flexibility, strength and jump
Background Isometric training is used in sport, conventional physical activity and rehabilitation. Understandably, there is a great deal of research related to its effect on performance. It is known that the length of the muscle at the moment of contraction is a determinant of strength levels. In the literature we find research on isometric training in short muscle lengths, although it has not been studied in maximally shortened positions or the acute effects that occur after its application. Ballistic stretching (BS) is also popular in sport. Their execution involves actively reaching maximally shortened muscle positions. So far, isometric training has not been compared with protocols involving ballistic stretching. Considering the above, the aim of the present study was to investigate the effects of BS and voluntary isometric contraction at maximal shortening (VICAMS) on range of motion, strength and vertical jump. Methods The study involved 60 healthy, physically active individuals (40 and 52 years old) who were randomly assigned to three groups: BS, VICAMS and a control group (CG). To assess acute effects, before and after the intervention, active range of motion (AROM), maximal voluntary isometric force (MVIF) and countermovement jump height (CMJ) were determined. Results Time main effects and time*group interactions were found for all variables (p < 0.001). Between-group differences were shown for the VICAMS group after the intervention, with statistically significant higher AROM values compared to the other groups. MVIF values were also higher in the VICAMS group. Intra-group differences were observed for the VICAMS and Ballistic groups, as values on all variables increased from baseline. For the CMJ, intra-group differences showed that both the VICAMS and BS groups improved values compared to baseline values. Conclusions The application of VICAMS induced acute improvements over BS in AROM, MVIF and CMJ. These results are important for coaches seeking immediate performance improvement and offer an optimal solution to the warm-up protocol.
Hernández-Trujillo et al. (2024) Acute effects of voluntary isometric contractions at maximal shortening vs. ballistic stretching on flexibility, strength and jump. PeerJ 12:e17819 https://doi.org/10.7717/peerj.17819
Low-dose hexavalent chromium induces mitophagy in rat liver via the AMPK-related PINK1/Parkin signaling pathway
Hexavalent chromium (Cr(VI)) is a hazardous metallic compound commonly used in industrial processes. The liver, responsible for metabolism and detoxification, is the main target organ of Cr(VI). Toxicity experiments were performed to investigate the impacts of low-dose exposure to Cr(VI) on rat livers. It was revealed that exposure of 0.05 mg/kg potassium dichromate (K2Cr2O7) and 0.25 mg/kg K2Cr2O7 notably increased malondialdehyde (MDA) levels and the expressions of P-AMPK, P-ULK, PINK1, P-Parkin, and LC3II/LC3I, and significantly reduced SOD activity and P-mTOR and P62 expression levels in liver. Electron microscopy showed that CR(VI) exposure significantly increased mitophagy and the destruction of mitochondrial structure. This study simulates the respiratory exposure mode of CR(VI) workers through intratracheal instillation of CR(VI) in rats. It confirms that autophagy in hepatocytes is induced by low concentrations of CR(VI) and suggest that the liver damage caused by CR(VI) may be associated with the AMPK-related PINK/Parkin signaling pathway.
Li et al. (2024) Low-dose hexavalent chromium induces mitophagy in rat liver via the AMPK-related PINK1/Parkin signaling pathway. PeerJ 12:e17837 https://doi.org/10.7717/peerj.17837
Stress induced on permanent mandible first molar and space maintainer under normal masticatory forces: a finite element study
Background The band and loop space maintainer is used to maintain the missing space of deciduous molars which are lost early. When the second deciduous molar is lost prematurely, the stress on the first permanent molar during different degrees of development may vary when it is the abutment. The design and use of the space maintainer may also lead to damage of the loop. The purpose of this article is to use the finite element method to study the stress on the first permanent molar and the loop with or without occlusal contact, with the first permanent molar of four different degrees of development serving as the abutment. We aimed to guide the clinical design and use of the space maintainer. Methods We developed finite element models of the mandibular first permanent molar and the band and loop space maintainer, and simulated alveolar bone, periodontal ligament (PDL), enamel and dentin. The four developmental stages were 1/2 (I), 2/3 (II), 3/4 (III) and full development (IV). Ansys Workbench was used to analyze the effects of root development and occlusal contact between the loop and the opposite jaw on abutment teeth and the loop. Abutment teeth were statically loaded vertically and obliquely with a force of 70 N. The loop was statically loaded vertically with a force of 14 N. The stress on all structures and the displacement trends of the loop were calculated. Results The stress on enamel, dentin, PDL and alveolar bone were similar, and the concentration was consistent. But if there was occlusal contact, the loop produced maximum displacement at the near middle edge of contact with the anterior teeth. When the loop was in occlusal contact with the opposing occlusal tooth, the peak value of the equivalent stress on the space maintainer under vertical load was: group I > group IV > group III > group II, and the maximum principal stress peak change was: group I > group III > group II > group IV. The change of the equivalent stress peak value of the loop under oblique load was: group I > group III > group IV > group II, and the maximum principal stress peak change was: group III > group I > group II > group IV. When the loop was not in occlusal contact with the opposing occlusal tooth, the peak value of the equivalent stress on the space maintainer under vertical load was: group IV > group I > group II > group III, and the maximum principal stress peak change was: group IV > group I > group II > group III. The change of the equivalent stress peak value of the space maintainer under oblique load was: group I > group IV > group II > group III, and the maximum principal stress peak change was: group I > group IV > group II > group III. Conclusions Our results suggested that whenever possible, choosing the teeth with nearly complete root development as the abutment of the space maintainer is advisable. The design and use of the band and loop space maintainer should avoid occlusal contact with the occlusal teeth to prevent deformation of the loop.
Shi et al. (2024) Stress induced on permanent mandible first molar and space maintainer under normal masticatory forces: a finite element study. PeerJ 12:e17456 https://doi.org/10.7717/peerj.17456
Curcumin improves atrial fibrillation susceptibility by regulating tsRNA expression in aging mouse atrium
Age is an independent risk factor for atrial fibrillation (AF), and curcumin can delay aging related disease through reducing oxidative stress and inflammation. However, its target in aging-related AF remains unclear. Transfer RNA-derived small RNA (tsRNA) is a novel short non-coding RNA (sncRNA), and exerts a potential regulatory function in aging. This study was to explore the therapeutic targets of curcumin in atrium of aged mice by PANDORA-seq. Aged mice (18 month) were treated with curcumin (100 mg/kg). Rapid transjugular atrial pacing was performed to observe AF inducibility. SA-β-gal staining, reactive oxygen species (ROS) detection and qRT-PCR were used to assess the degree of aging and oxidative stress/inflammation levels. PANDORA-seq was performed to reveal the differentially expressed sncRNAs in the atrium of mice. The results showed that curcumin reduced the susceptibility AF of aged mice by improving aging-related atrial fibrosis. Compared to young mice (5 month) group, aged mice yielded 473 significantly altered tsRNA sequences, while 947 tsRNA sequences were significantly altered after treated with curcumin. Enrichment analysis revealed that the target genes were mainly related to DNA damage and protein modification. Compared with the 5 month group, the expression levels of mature-mt_tRNA-Val-TAC_CCA_end, mature-mt_tRNA-Glu-TTC_CCA_end, and mature-tRNA-Asp-GTC_CCA_end were up-regulated in the 18 month group, while the expression of mature-mt_tRNA-Thr-TGT_5_end was down-regulated. This trend was reversed in the 18 month + curcumin group. Increased cellular ROS levels, inflammation expression and senescence in aged mice atrium were improved by the down-regulation of mature-mt_tRNA-Val-TAC_CCA_end. In conclusion, our findings identified mature-mt_tRNA-Val-TAC_CCA_end participated in the mechanism of aging-related atrial fibrosis, providing new intervention target of aging-related AF.
Luo et al. (2024) Curcumin improves atrial fibrillation susceptibility by regulating tsRNA expression in aging mouse atrium. PeerJ 12:e17495 https://doi.org/10.7717/peerj.17495
Identification of the RRM1 gene family in rice (Oryza sativa) and its response to rice blast
To better understand RNA-binding proteins in rice, a comprehensive investigation was conducted on the RRM1 gene family of rice. It encompassed genome-wide identification and exploration of its role in rice blast resistance. The physicochemical properties of the rice OsRRM1 gene family were analyzed. There genes were also analyzed for their conserved domains, motifs, location information, gene structure, phylogenetic trees, collinearity, and cis-acting elements. Furthermore, alterations in the expression patterns of selected OsRRM1 genes were assessed using quantitative real-time PCR (qRT-PCR). A total of 212 members of the OsRRM1 gene family were identified, which were dispersed across 12 chromosomes. These genes all exhibit multiple exons and introns, all of which encompass the conserved RRM1 domain and share analogous motifs. This observation suggests a high degree of conservation within the encoded sequence domain of these genes. Phylogenetic analysis revealed the existence of five subfamilies within the OsRRM1 gene family. Furthermore, investigation of the promoter region identified cis-regulatory elements that are involved in nucleic acid binding and interaction with multiple transcription factors. By employing GO and KEGG analyses, four RRM1 genes were tentatively identified as crucial contributors to plant immunity, while the RRM1 gene family was also found to have a significant involvement in the complex of alternative splicing. The qRT-PCR results revealed distinct temporal changes in the expression patterns of OsRRM1 genes following rice blast infection. Additionally, gene expression analysis indicates that the majority of OsRRM1 genes exhibited constitutive expressions. These findings enrich our understanding of the OsRRM1 gene family. They also provide a foundation for further research on immune mechanisms rice and the management of rice blast.
Jiang et al. (2024) Identification of the RRM1 gene family in rice (Oryza sativa) and its response to rice blast. PeerJ 12:e17668 https://doi.org/10.7717/peerj.17668
Psycho-physio-neurological correlates of qualitative attention, emotion and flow experiences in a close-to-real-life extreme sports situation: low- and high-altitude slackline walking
It has been indicated that extreme sport activities result in a highly rewarding experience, despite also providing fear, stress and anxiety. Studies have related this experience to the concept of flow, a positive feeling that individuals undergo when they are completely immersed in an activity. However, little is known about the exact nature of these experiences, and, there are still no empirical results to characterize the brain dynamics during extreme sport practice. This work aimed at investigating changes in psychological responses while recording physiological (heart rate–HR, and breathing rate–BR) and neural (electroencephalographic–EEG) data of eight volunteers, during outdoors slackline walking in a mountainous environment at two different altitude conditions (1 m–low-walk– and 45 m–high-walk–from the ground). Low-walk showed a higher score on flow scale, while high-walk displayed a higher score in the negative affect aspects, which together point to some level of flow restriction during high-walk. The order of task performance was shown to be relevant for the physiological and neural variables. The brain behavior during flow, mainly considering attention networks, displayed the stimulus-driven ventral attention network–VAN, regionally prevailing (mainly at the frontal lobe), over the goal-directed dorsal attention network–DAN. Therefore, we suggest an interpretation of flow experiences as an opened attention to more changing details in the surroundings, i.e., configured as a ‘task-constantly-opened-to-subtle-information experience’, rather than a ‘task-focused experience’.
de Sampaio Barros et al. (2024) Psycho-physio-neurological correlates of qualitative attention, emotion and flow experiences in a close-to-real-life extreme sports situation: low- and high-altitude slackline walking. PeerJ 12:e17743 https://doi.org/10.7717/peerj.17743
DTDHM: detection of tandem duplications based on hybrid methods using next-generation sequencing data
Background Tandem duplication (TD) is a common and important type of structural variation in the human genome. TDs have been shown to play an essential role in many diseases, including cancer. However, it is difficult to accurately detect TDs due to the uneven distribution of reads and the inherent complexity of next-generation sequencing (NGS) data. Methods This article proposes a method called DTDHM (detection of tandem duplications based on hybrid methods), which utilizes NGS data to detect TDs in a single sample. DTDHM builds a pipeline that integrates read depth (RD), split read (SR), and paired-end mapping (PEM) signals. To solve the problem of uneven distribution of normal and abnormal samples, DTDHM uses the K-nearest neighbor (KNN) algorithm for multi-feature classification prediction. Then, the qualified split reads and discordant reads are extracted and analyzed to achieve accurate localization of variation sites. This article compares DTDHM with three other methods on 450 simulated datasets and five real datasets. Results In 450 simulated data samples, DTDHM consistently maintained the highest F1-score. The average F1-score of DTDHM, SVIM, TARDIS, and TIDDIT were 80.0%, 56.2%, 43.4%, and 67.1%, respectively. The F1-score of DTDHM had a small variation range and its detection effect was the most stable and 1.2 times that of the suboptimal method. Most of the boundary biases of DTDHM fluctuated around 20 bp, and its boundary deviation detection ability was better than TARDIS and TIDDIT. In real data experiments, five real sequencing samples (NA19238, NA19239, NA19240, HG00266, and NA12891) were used to test DTDHM. The results showed that DTDHM had the highest overlap density score (ODS) and F1-score of the four methods. Conclusions Compared with the other three methods, DTDHM achieved excellent results in terms of sensitivity, precision, F1-score, and boundary bias. These results indicate that DTDHM can be used as a reliable tool for detecting TDs from NGS data, especially in the case of low coverage depth and tumor purity samples.
Yuan et al. (2024) DTDHM: detection of tandem duplications based on hybrid methods using next-generation sequencing data. PeerJ 12:e17748 https://doi.org/10.7717/peerj.17748