Depression and low physical activity are related to sarcopenia in hemodialysis: a single-center study
Background The number of patients who suffer from chronic renal failure (CRF) has widely increased worldwide. Patients with advanced stages of CRF experience a gradual and progressive loss of muscle and fat mass leading to decreased physical activity and mental health problems. The loss of muscle mass in CRF might contribute to the development of sarcopenia. Therefore, this study aimed to explore the prevalence of sarcopenia and to determine the relationship of physical activity and mental state of depression with sarcopenia in hemodialysis patients. Methods A cross-sectional study was designed with a total of 104 male and female with a minimum age of 35 years. Based on the guidelines of the Asian Working Group for Sarcopenia in 2019, gait speed, muscle mass, and handgrip were used to define sarcopenia. In addition, participants were requested to perform a set of questionnaires to evaluate their physical activity and state of depression. Logistic regression analyses were used to explore the risk factors of sarcopenia. Results Thirty-four (32.69%) of 104 participants had sarcopenia. Compared to the 70 individuals without sarcopenia, they had a low physical activity and a high depression score (ps < .05). Furthermore, low physical activity and high depression scores in combination with sarcopenia were associated with an increased mortality risk. Low physical activity and high depression scores were also independently associated with sarcopenia in hemodialysis patients after controlling for age (odds ratio = 3.23, and 4.92, respectively).
Yuenyongchaiwat et al. (2021) Depression and low physical activity are related to sarcopenia in hemodialysis: a single-center study. PeerJ 9:e11695 https://doi.org/10.7717/peerj.11695
Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study
Background Early and accurate diagnosis of microorganism(s) is important to optimize antimicrobial therapy. Shotgun metagenomic sequencing technology, an unbiased and comprehensive method for pathogen identification, seems to potentially assist or even replace conventional microbiological methodology in the diagnosis of infectious diseases. However, evidence in clinical application of this platform is relatively limited. Methods To evaluate the capability of shotgun metagenomic sequencing technology in clinical practice, both shotgun metagenomic sequencing and conventional culture were performed in the PCR-positive body fluid specimens of 20 patients with suspected infection. The sequenced data were then analyzed for taxonomic identification of microbes and antibiotic resistance gene prediction using bioinformatics pipeline. Results Shotgun metagenomic sequencing results showed a concordance of 17/20 compared with culture results in bacterial detection, and a concordance of 20/20 compared with culture results in fungal detection. Besides, drug-resistant types annotated from antibiotic resistance genes showed much similarity with antibiotic classes identified by susceptibility tests, and more than half of the specimens had consistent drug types between shotgun metagenomic sequencing and culture results. Conclusions Pathogen identification and antibiotic resistance gene prediction by shotgun metagenomic sequencing identification had the potential to diagnose microorganisms in infectious diseases, and it was especially helpful for multiple microbial co-infections and for the cases where standard culture approached failed to identify microorganisms.
Chen et al. (2021) Identification of pathogen(s) in infectious diseases using shotgun metagenomic sequencing and conventional culture: a comparative study. PeerJ 9:e11699 https://doi.org/10.7717/peerj.11699
Identification of a three-gene-based prognostic model in multiple myeloma using bioinformatics analysis
Background Multiple myeloma (MM), the second most hematological malignancy, has high incidence and remains incurable till now. The pathogenesis of MM is poorly understood. This study aimed to identify novel prognostic model for MM on gene expression profiles. Methods Gene expression datas of MM (GSE6477, GSE136337) were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in GSE6477 between case samples and normal control samples were screened by the limma package. Meanwhile, enrichment analysis was conducted, and a protein-protein interaction (PPI) network of these DEGs was established by STRING and cytoscape software. Co-expression modules of genes were built by Weighted Correlation Network Analysis (WGCNA). Key genes were identified both from hub genes and the DEGs. Univariate and multivariate Cox congression were performed to screen independent prognostic genes to construct a predictive model. The predictive power of the model was evaluated by Kaplan–Meier curve and time-dependent receiver operating characteristic (ROC) curves. Finally, univariate and multivariate Cox regression analyse were used to investigate whether the prognostic model could be independent of other clinical parameters. Results GSE6477, including 101 case and 15 normal control, were screened as the datasets. A total of 178 DEGs were identified, including 59 up-regulated and 119 down-regulated genes. In WGCNA analysis, module black and module purple were the most relevant modules with cancer traits, and 92 hub genes in these two modules were selected for further analysis. Next, 47 genes were chosen both from the DEGs and hub genes as key genes. Three genes (LYVE1, RNASE1, and RNASE2) were finally screened by univariate and multivariate Cox regression analyses and used to construct a risk model. In addition, the three-gene prognostic model revealed independent and accurate prognostic capacity in relation to other clinical parameters for MM patients. Conclusion In summary, we identified and constructed a three-gene-based prognostic model that could be used to predict overall survival of MM patients.
Pan et al. (2021) Identification of a three-gene-based prognostic model in multiple myeloma using bioinformatics analysis. PeerJ 9:e11320 https://doi.org/10.7717/peerj.11320
Physiological, nutritional, and molecular responses of Brazilian sugarcane cultivars under stress by aluminum
Background Sugarcane is a crop of global importance and has been expanding to areas with soils containing high levels of exchangeable aluminum (Al), which is a limiting factor for crop development in acidic soils. The study of the sugarcane physiological and nutritional behavior together with patterns of gene expression in response to Al stress may provide a basis for effective strategies to increase crop productivity in acidic soils. Methods Sugarcane cultivars were evaluated for physiological parameters (photosynthesis, stomatal conductance, and transpiration), nutrient (N, P, K, Ca, Mg, and S) and Al contents in leaves and roots and gene expression, of the genes MDH, SDH by qPCR, both related to the production of organic acids, and SOD, related to oxidative stress. Results Brazilian sugarcane RB867515, RB928064, and RB935744 cultivars exhibited very different responses to induced stress by Al. Exposure to Al caused up-regulation (SOD and MDH) or down-regulation (SDH, MDH, and SOD), depending on the cultivar, Al level, and plant tissue. The RB867515 cultivar was the most Al-tolerant, showing no decline of nutrient content in plant tissue, photosynthesis, transpiration, and stomatal conductance after exposure to Al; it exhibited the highest Al content in the roots, and showed important MDH and SOD gene expression in the roots. RB928064 only showed low expression of SOD in roots and leaves, while RB935744 showed important expression of the SOD gene only in the leaves. Sugarcane cultivars were classified in the following descending Al-tolerance order: RB867515 > RB928064 = RB935744. These results may contribute to the obtention of Al-tolerant cultivars that can play their genetic potential in soils of low fertility and with low demand for agricultural inputs; the selection of potential plants for breeding programs; the elucidation of Al detoxification mechanisms employed by sugarcane cultivars.
Oliveira et al. (2021) Physiological, nutritional, and molecular responses of Brazilian sugarcane cultivars under stress by aluminum. PeerJ 9:e11461 https://doi.org/10.7717/peerj.11461
Effects of biotransport and hydro-meteorological conditions on transport of trace elements in the Scott River (Bellsund, Spitsbergen)
The shaping of surface water chemistry in the Svalbard Archipelago is strongly dependent on the geology of the catchment and the process of long-range transport of atmospheric pollutants (LRATP). It was found that the dissolved trace elements in the Scott River, which catchment is characterized by a decreasing degree of glaciation, were of the natural origin (i.a. weathering and dissolution of local geological substratum). The exception was Zn originated from LRATP. The paper describe the influence changes in hydro-meteorological conditions and the presence of a seabird colony on the variability in the transport of trace elements within the Scott River catchment. The work assesses long-time fluctuations in the concentration of twenty five trace elements (i.a. Al, Cr, Cu, Pb, Sr, and Zn) from eighty-four surface water samples and their relation to changes in water discharge (Q), precipitation (P), pH, and dissolved organic carbon (DOC) at two river sites (with one being under the influence of the biotransport factor). Based on the results of matrix correlation and cluster analysis it was found that the additional load of DOC from the nesting site of Larus Argentatus in the mouth section of the river drastically changed the hydro-geochemical cycle of Co, Ni, Zn, Ga, Sr, Rb, Ba and U (0.30 < r < 0.51). Furthermore, the results of cluster analysis confirmed that the bird colony’s nesting site was strongly responsible for the presence of U, Rb, Zn, Ni and marine-derived nutrients (e.g. Se and Li). The discharge of glacier meltwater and the alkaline character of water have a negative effect on the dissolution of Li and Mn (−0.31 < r < −0.51), but positively affect the level of Rb and U (r = 0.31 and 0.35, respectively) due to it being washing out a seabird nesting colony in the mouth section of the Scott River. It was observed that the event of rises in air temperature and rain, which results in increased water discharge, caused an intense transport of the trace elements load. Moreover, results of the precipitation sensitivity coefficient factor (CF) proved that precipitation effect the occurrence of Li, Sr and U in the Scott River.
Environmental Contamination and Remediation
Lehmann-Konera et al. (2021) Effects of biotransport and hydro-meteorological conditions on transport of trace elements in the Scott River (Bellsund, Spitsbergen). PeerJ 9:e11477 https://doi.org/10.7717/peerj.11477
Characterization of the microbiome of the invasive Asian toad in Madagascar across the expansion range and comparison with a native co-occurring species
Biological invasions are on the rise, with each invader carrying a plethora of associated microbes. These microbes play important, yet poorly understood, ecological roles that can include assisting the hosts in colonization and adaptation processes or as possible pathogens. Understanding how these communities differ in an invasion scenario may help to understand the host’s resilience and adaptability. The Asian common toad, Duttaphrynus melanostictus is an invasive amphibian, which has recently established in Madagascar and is expected to pose numerous threats to the native ecosystems. We characterized the skin and gut bacterial communities of D. melanostictus in Toamasina (Eastern Madagascar), and compared them to those of a co-occurring native frog species, Ptychadena mascareniensis, at three sites where the toad arrived in different years. Microbial composition did not vary among sites, showing that D. melanostictus keeps a stable community across its expansion but significant differences were observed between these two amphibians. Moreover, D. melanostictus had richer and more diverse communities and also harboured a high percentage of total unique taxa (skin: 80%; gut: 52%). These differences may reflect the combination of multiple host-associated factors including microhabitat selection, skin features and dietary preferences.
Santos et al. (2021) Characterization of the microbiome of the invasive Asian toad in Madagascar across the expansion range and comparison with a native co-occurring species. PeerJ 9:e11532 https://doi.org/10.7717/peerj.11532
Helicobacter pylori prevalence in healthy Mexican children: comparison between two non-invasive methods
Background Helicobacter pylori detection in asymptomatic children with suspected infection or with symptoms that suggest gastric pathology is problematic, since most of the methods depend on the endoscopic study, an invasive and expensive method. Non-invasive methods can be a feasible alternative but must be validated. The purpose of this study was to evaluate the concordance between H. pylori DNA detection in saliva and dental plaque by PCR, with antigen detection in stool by immunochromatography, among asymptomatic children in the state of Guerrero, Mexico. Methods Dental plaque, saliva, and stool samples were obtained from 171 children between 6 and 12 years old. H. pylori detection in saliva and dental plaque was performed by PCR using specific primers for the 16S rRNA gene, while the detection in stool samples was performed by immunochromatography using the CerTest kit. Results We found an overall H. pylori prevalence of 59.6% (102/171). Of the H. pylori positive children 18% (20/111) were positive in saliva samples, 28.1% (34/121) in dental plaque samples, and 50.4% (71/141) in stool samples. A higher prevalence was found in girls (64.7%, p = 0.002). Although some of the children declared some dyspeptic symptoms, these were no related to H. pylori. In conclusion, we found a high prevalence of H. pylori in asymptomatic children and the highest proportion was detected by stool antigen test, which was the most feasible method to detect H. pylori infection.
Martínez-Santos et al. (2021) Helicobacter pylori prevalence in healthy Mexican children: comparison between two non-invasive methods. PeerJ 9:e11546 https://doi.org/10.7717/peerj.11546
Iron deficiency anemia among children aged 2–5 years in southern Ethiopia: a community-based cross-sectional study
Background Iron-deficiency anemia (IDA) is a common type of nutritional anemia in low-income countries, including Ethiopia. However, there is limited data on iron deficiency anemia prevalence and associated factors in Ethiopia, particularly for children aged 2 to 5 years. Objectives To establish the prevalence of iron deficiency anemia and associated risk factors, focusing on iron-rich food consumption among children aged 2 to 5 years in southern Ethiopia. Methods A community-based cross-sectional study was conducted in southern Ethiopia in 2017, involving 331 randomly selected children aged 2 to 5 years old. A structured questionnaire was used to collect information about the children and the households. Venous blood was collected from each child in a test tube to measure hemoglobin, ferritin, and C-reactive protein (CRP). Hemoglobin levels were determined using Hemocue®301 and adjusted for altitude. Anemia was defined as hemoglobin levels <11 g/dl. Ferritin was adjusted for inflammation based on CRP concentration and low ferritin concentration defined as adjusted ferritin concentration <12 µg/L. IDA was considered when a child had both hemoglobin level <11g/dl and low ferritin concentration. Bi-variable and multivariable logistic regression models were performed to identify factors associated with IDA and iron-rich food consumption. Results The prevalence of iron deficiency anemia was 25%, and the total anemia prevalence was 32%. Only 15% of children consumed iron-rich foods in the preceding 24 h, and 30% of children consumed iron-rich foods at least once in the preceding week. IDA decreased as the height for age z-score increased (Adjusted Odds Ratio 0.7; 95% CI [0.5–0.9]). Mothers with increased educational level (AOR 1.1; 1.0–1.2) and households with increased dietary diversity (AOR 1.4; 1.2–1.6) consumed more iron-rich foods. Conclusions Iron deficiency anaemia was a moderate public health problem in southern Ethiopia, and the iron-rich food consumption was low. Interventions should focus on food supplementation and fortification, food diversification and nutritional education, and promoting women’s education.
Orsango et al. (2021) Iron deficiency anemia among children aged 2–5 years in southern Ethiopia: a community-based cross-sectional study. PeerJ 9:e11649 https://doi.org/10.7717/peerj.11649
Combination of ferulic acid, ligustrazine and tetrahydropalmatine inhibits invasion and metastasis through MMP/TIMP signaling in endometriosis
Background The design of the combination of ferulic acid, ligustrazine and tetrahydropalmatine (FLT) is inspired by the Chinese herbal prescription Foshou San. Previous work has shown that FLT inhibited endometriosis growth in rat autograft models. However, the mechanism behind this is unclear. MMP/TIMP signaling is considered as the vital pathway of metastasis and invasion in endometriosis. In this study, we aim to disclose effects of FLT on MMP/TIMP signaling in invasion and metastasis during endometrial cells and xenograft endometriosis. Methods In vivo, effect of FLT on endometriosis was evaluated in a xenogeneic mice model. In vitro, cell viability assay was performed with an IC50 measurement of FLT in hEM15A and HEC1-B cells. The effect of FLT on invasion and metastasis was analyzed in scratch wound and transwell assay. Gene and protein expression of MMP/TIMP signaling were detected by qPCR and Western blotting. Results In xenograft endometriosis, FLT reduced ectopic volume without effect on weight. FLT inhibitory effects on cell growth exhibited a dose-dependent manner in hEM15A and HEC1-B cells. IC50s of FLT in hEM15A cells were 839.30 ± 121.11 or 483.53 ±156.91 μg·ml−1 after the treatment for 24 or 48 h, respectively. In HEC1-B cells, IC50 values of 24 or 48 h were 625.20 ± 59.52 or 250.30 ± 68.12 μg·ml−1. In addition, FLT significantly inhibited invasion and metastasis in scratch wound and transwell assay. Furthermore, FLT inactivated MMP/TIMP signaling with decreasing expression of MMP-2/9, and an enhancing expression of TIMP-1. Conclusions MMP/TIMP inactivation is a reasonable explanation for the inhibition of FLT on invasion and metastasis in endometriosis. This result reveals a potential mechanism on the role of FLT in endometriosis and may benefit for its further application.
Tan et al. (2021) Combination of ferulic acid, ligustrazine and tetrahydropalmatine inhibits invasion and metastasis through MMP/TIMP signaling in endometriosis. PeerJ 9:e11664 https://doi.org/10.7717/peerj.11664
Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize
As one of the major crops, maize (Zea mays L.) is mainly distributed in tropical and temperate regions. However, with the changes of the environments, chilling stress has become a significantly abiotic stress affecting seed germination and thus the reproductive and biomass accumulation of maize. Herein, we investigated five seed germination-related phenotypes among 300 inbred lines under low-temperature condition (10 °C). By combining 43,943 single nucleotide polymorphisms (SNPs), a total of 15 significant (P < 2.03 × 10-6) SNPs were identified to correlate with seed germination under cold stress based on the FarmCPU model in GWAS, among which three loci were repeatedly associated with multiple traits. Ten gene models were closely linked to these three variations, among which Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021 were further verified by candidate gene association study and expression pattern analysis. Importantly, these candidate genes were previously reported to involve plant tolerance to chilling stress and other abiotic stress. Our findings contribute to the understanding of the genetic and molecular mechanisms underlying chilling germination in maize.
Zhang et al. (2021) Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize. PeerJ 9:e11707 https://doi.org/10.7717/peerj.11707