Methylation of CYP1A1 and VKORC1 promoter associated with stable dosage of warfarin in Chinese patients
Objective To investigate the association between DNA methylation and the stable warfarin dose through genome-wide DNA methylation analysis and pyrosequencing assay. Method This study included 161 patients and genome-wide DNA methylation analysis was used to screen potential warfarin dose-associated CpGs through Illumina Infinium HumanMethylation 450 K BeadChip; then, the pyrosequencing assay was used to further validate the association between the stable warfarin dose and alterations in the methylation of the screened CpGs. GenomeStudio Software and R were used to analyze the differentially methylated CpGs. Results The methylation levels of CpGs surrounding the xenobiotic response element (XRE) within the CYP1A1 promoter, differed significantly between the different dose groups (P < 0.05), and these CpGs presented a positive correlation (r> 0, P < 0.05) with an increase in the stable dose of warfarin. At the VKORC1 promoter, two CpGs methylation levels were significantly different between the differential dose groups (P < 0.05), and one CpG (Chr16: 31106793) presented a significant negative correlation (r < 0, P < 0.05) among different dose (low, medium, and high) groups. Conclusion This is a novel report of the methylation levels of six CpGs surrounding the XRE within the CYP1A1 promoter and one differential CpG at the VKORC1 promoter associated with stable warfarin dosage; these methylation levels might be applied as molecular signatures for warfarin.
He et al. (2021) Methylation of CYP1A1 and VKORC1 promoter associated with stable dosage of warfarin in Chinese patients. PeerJ 9:e11549 https://doi.org/10.7717/peerj.11549
Host migration and environmental temperature influence avian haemosporidians prevalence: a molecular survey in a Brazilian Atlantic rainforest
Avian haemosporidians are parasites with great capacity to spread to new environments and new hosts, being considered a good model to host-parasite interactions studies. Here, we examine avian haemosporidian parasites in a protected area covered by Restinga vegetation in northeastern Brazil, to test the hypothesis that haemosporidian prevalence is related to individual-level traits (age and breeding season), species-specific traits (diet, foraging strata, period of activity, species body weight, migratory status, and nest shape), and climate factors (temperature and rainfall). We screened DNA from 1,466 birds of 70 species captured monthly from April 2013 to March 2015. We detected an overall prevalence (Plasmodium/Haemoproteus infection) of 22% (44 host species) and parasite’s lineages were identified by mitochondrial cyt b gene. Our results showed that migration can be an important factor predicting the prevalence of Haemoproteus (Parahaemoproteus), but not Plasmodium, in hosts. Besides, the temperature, but not rainfall, seems to predict the prevalence of Plasmodium in this bird community. Neither individual-level traits analyzed nor the other species-specific traits tested were related to the probability of a bird becoming infected by haemosporidians. Our results point the importance of conducting local studies in particular environments to understand the degree of generality of factors impacting parasite prevalence in bird communities. Despite our attempts to find patterns of infection in this bird community, we should be aware that an avian haemosporidian community organization is highly complex and this complexity can be attributed to an intricate net of factors, some of which were not observed in this study and should be evaluated in future studies. We evidence the importance of looking to host-parasite relationships in a more close scale, to assure that some effects may not be obfuscated by differences in host life-history.
Rodrigues et al. (2021) Host migration and environmental temperature influence avian haemosporidians prevalence: a molecular survey in a Brazilian Atlantic rainforest. PeerJ 9:e11555 https://doi.org/10.7717/peerj.11555
The protective effect of Moringa oleifera plant extract against glutamate-induced DNA damage and reduced cell viability in a primary retinal ganglion cell line
Background Glutamate excitotoxicity can cause DNA damage and is linked to many retinal and neurological disorders. In mammals, the visual signal from the eyes to the brain is conducted only by retinal ganglion cells (RGCs), which can be damaged by overstimulation of glutamate receptors. Methodology We examined the protective effects of Moringa oleifera seed extract against glutamate-induced DNA damage in RGCs. RGCs cells were treated with 5, 10, 50, or 100 µg/ml of M. oleifera seed extract and glutamate separately and then assessed for DNA damage using the comet assay. We also evaluated the viability of the RGCs after both treatments using the MTT test. Additionally, RGCs were pretreated with M. oleifera seed extract (50 or 100 µg/ml) for 2 h before glutamate treatment (100 µg/ml) to determine the potential protective effects of M. oleifera. We performed a phytochemical analysis of the M. oleifera seed extract using standard reactions. Results The M. oleifera seed extract was found to be rich in many phytochemicals. We observed a significant dose-dependent elevation in all comet assay variables in glutamate-treated RGCs, whereas M. oleifera seed extract treatments did not show any significant change in DNA integrity. Conclusion M. oleifera seed extract demonstrates neuroprotective effects, which suggests it may help to prevent the development of many neurodegenerative disorders.
Amina et al. (2021) The protective effect of Moringa oleifera plant extract against glutamate-induced DNA damage and reduced cell viability in a primary retinal ganglion cell line. PeerJ 9:e11569 https://doi.org/10.7717/peerj.11569
Comparative anatomical and transcriptomic analyses of the color variation of leaves in Aquilaria sinensis
Color variation in plant tissues is a common phenomenon accompanied with a series of biological changes. In this study, a special-phenotype Aquilaria sinensis (GS) with color variation of leaf was firstly reported, and DNA barcode sequences showed GS samples could not be discriminated clearly with the normal A. sinensis sample (NS), which suggested that the variety was not the cause of the GS formation. To reveal the characteristics of GS compared to NS, the anatomical and transcriptome sequencing studies were carried out. In microscopic observation, the leaves of golden-vein-leaf sample (LGS) and normal-vein-leaf sample (LNS) showed significant differences including the area of the included phloem in midrib and the thickness parameters of palisade and spongy tissues; the stems of golden-vein-leaf sample (SGS) and normal-vein-leaf sample (SNS) were also different in many aspects such as the area of vessels and included phloem. In addition, the structure of chloroplast was more complete in the midrib of LNS than that of LGS, and some particles suspected as virus were found through transmission electron microscope as well. Genes upregulated in LGS in contrast with LNS were mainly enriched in photosynthesis. As for stems, most of the genes upregulated in SGS compared to SNS were involved in translation and metabolism processes. The pathways about photosynthesis and chlorophyll metabolism as well as some important transcription factors may explain the molecular mechanism of the unique phenotypes of leaves and the genes related to suberin biosynthesis may result in the difference of stems. In addition, the genes about defense response especially biotic stress associated with numerous pathogenesis-related (PR) genes upregulated in LGS compared to LNS indicated that the pathogen may be the internal factor. Taken together, our results reveal the macro- and micro-phenotype variations as well as gene expression profiles between GS and NS, which could provide valuable clues for elucidating the mechanism of the color variation of Aquilaria.
Gao et al. (2021) Comparative anatomical and transcriptomic analyses of the color variation of leaves in Aquilaria sinensis. PeerJ 9:e11586 https://doi.org/10.7717/peerj.11586
Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)
Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.
Tomar et al. (2021) Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.). PeerJ 9:e11593 https://doi.org/10.7717/peerj.11593
Continued nucleic acid tests for SARS-CoV-2 following discharge of patients with COVID-19 in Lu’an, China
Background Studies have shown that discharged Coronavirus disease 2019 (COVID-19) patients have retested positive for SARS-CoV-2 during a follow-up RT-PCR test. We sought to assess the results of continued nucleic acid testing for SARS-CoV-2 patients in COVID-19 patients after they were discharged in Lu’an, China. Methods We conducted RT-PCR tests on sputum, throat swabs, fecal or anal swabs, and urine samples collected from 67 COVID-19 patients following discharge. Samples were collected on the 7th and 14th days following discharge. Patients testing positive on the 7th or 14th day were retested after 24 hours until they tested negative twice. Results Seventeen (17/67, 25.4%) discharged COVID-19 patients had a positive RT-PCR retest for SARS-CoV-2. Among them, 14 (82.4%) were sputum positive, five (29.4%) were throat swab positive, seven (41.2%) were fecal or anal swab positive, one (5.9%) was urine sample positive, five (29.4%) were both sputum and throat swab positive, four (23.5%) were both sputum and fecal test positive, and one (5.9%) was positive of all four specimens. The shortest period of time between discharge and the last positive test was 7 days, the longest was 48 days, and the median was 16 days. The proportion of positive fecal or anal swab tests increased from the third week. The median Cq cut-off values after onset were 26.7 after the first week, 37.7 the second to sixth week, and 40 after the sixth week. There were no significant differences between the RT-PCR retest positive group and the unrecovered positive group. Conclusions There was a high proportion of patients who retested positive for COVID-19. Discharge criteria have remained fairly consistent so we encourage regions affected by COVID-19 to appropriately amend their current criteria.
Lyu et al. (2021) Continued nucleic acid tests for SARS-CoV-2 following discharge of patients with COVID-19 in Lu’an, China. PeerJ 9:e11617 https://doi.org/10.7717/peerj.11617
Potency of bisresorcinol from Heliciopsis terminalis on skin aging: in vitro bioactivities and molecular interactions
Background A bisresorcinol was isolated as the main constituent of Heliciopsis terminalis’s trunk (Proteaceae). Recently, resorcinol is applied as an active whitening agent in various cosmetic products. Because of the structural mimic to resorcinol, benefits of the bisresorcinol as an aging-enzyme antagonist were demonstrated in this study. Methods The bisresorcinol was purified from the crude ethanolic extract of H. terminalis’s trunk by solvent extraction and preparative chromatography, respectively. Inhibitory activity on collagenase, elastase, and tyrosinase of the compound was investigated by using a different spectroscopic technique. Molecular docking was carried out to predict possible interactions of the substance around the enzyme active sites. Results The IC50 values on collagenase of the bisresorcinol and caffeic acid were 156.7 ± 0.7 and 308.9 ± 1.6 µmole L−1, respectively. For elastase activity, the IC50 of 33.2 ± 0.5 and 34.3 ± 0.3 µmole L−1 was respectively determined for the bisresorcinol and ursolic acid. The bisresorcinol was inhibitory to tyrosinase by exhibiting the IC50 of 22.8 µmole L−1, and that of 78.4 µmole L−1 was present for β-arbutin. The bisresorcinol bound to collagenase, elastase, and tyrosinase with the respective binding energies of −5.89, −5.69, and −6.57 kcal mol−1. These binding energies were in the same ranges of tested inhibitors. The aromatic phenol groups in the structure were responsible for principle as well as supporting binding interactions with enzymes. Hydrogen binding due to hydroxyl groups and π-related attractive forces from an aromatic ring(s) provided binding versatility to bisresorcinol. Conclusion The bisresorcinol purified from H. terminalis might be useful for inclusion in cosmetic products as an aging-enzyme antagonist.
Saechan et al. (2021) Potency of bisresorcinol from Heliciopsis terminalis on skin aging: in vitro bioactivities and molecular interactions. PeerJ 9:e11618 https://doi.org/10.7717/peerj.11618
Evaluating active versus passive sources of human brucellosis in Jining City, China
Human brucellosis (HB) remains a serious public health concern owing to its resurgence across the globe and specifically in China. The timely detection of this disease is the key to its prevention and control. We sought to describe the differences in the demographics of high-risk populations with detected cases of HB contracted from active versus passive sources. We collected data from a large sample population from January to December 2018, in Jining City, China. We recruited patients that were at high-risk for brucellosis from three hospitals and Centers of Disease Control and Prevention (CDCs). These patients were classified into two groups: the active detection group was composed of individuals receiving brucellosis counseling at the CDCs; the passive detection group came from hospitals and high-risk HB groups. We tested a total of 2,247 subjects and 13.3% (299) presented as positive for HB. The positive rates for active and passive detection groups were 20.5% (256/1,249) and 4.3% (43/998), respectively (p < 0.001). The detection rate of confirmed HB cases varied among all groups but was higher in the active detection group than in the passive detection group when controlled for age, sex, ethnicity, education, career, and contact history with sheep or cattle (p < 0.05). Males, farmers, those with four types of contact history with sheep or cattle, and those presenting fever, hyperhidrosis and muscle pain were independent factors associated with confirmed HB cases in multivariate analysis of the active detection group. Active detection is the most common method used to detect brucellosis cases and should be applied to detect HB cases early and avoid misdiagnosis. We need to improve our understanding of brucellosis for high-risk populations. Passive HB detection can be supplemented with active detection when the cognitive changes resulting from brucellosis are low. It is important that healthcare providers understand and emphasis the timely diagnosis of HB.
Sun et al. (2021) Evaluating active versus passive sources of human brucellosis in Jining City, China. PeerJ 9:e11637 https://doi.org/10.7717/peerj.11637
Accuracy of triggering receptor expressed on myeloid cells 1 in diagnosis and prognosis of acute myocardial infarction: a prospective cohort study
Background Acute myocardial infarction (AMI) is one of the fatal cardiac emergencies. The detection of triggering receptor expressed on myeloid cells 1 (TREM1), a cell surface immunoglobulin that amplifies pro-inflammatory responses, screened by bioinformatics was shown to be significant in diagnosing and predicting the prognosis of AMI. Methods GSE66360, GSE61144 and GSE60993 were downloaded from the Gene Expression Omnibus (GEO) database to explore the differentially expressed genes (DEGs) between AMI and control groups using R software. A total of 147 patients in total were prospectively enrolled from October 2018 to June 2019 and divided into two groups, the normal group (n = 35) and the AMI group (n = 112). Plasma was collected from each patient at admission and all patients received 6-month follow-up care. Results According to bioinformatic analysis, TREM1 was an important DEG in patients with AMI. Compared with the normal group, TREM1 expression was markedly increased in the AMI group (p < 0.001). TREM1 expression was positively correlated with fasting plasma glucose (FPG), glycosylated hemoglobin (HbAC), and the number of lesion vessels, although it had no correlation with Gensini score. TREM1 expression in the triple-vessels group was significantly higher than that of the single-vessel group (p < 0.05). Multiple linear regression showed that UA and HbAC were two factors influencing TREM1 expression. The ROC curve showed that TREM1 had a diagnostic significance in AMI (p < 0.001), especially in AMI patients without diabetes. Cox regression showed increased TREM1 expression was closely associated with 6-month major adverse cardiac events (MACEs) (p < 0.001). Conclusions TREM1 is a potentially significant biomarker for the diagnosis of AMI and may be closely associated with the severity of coronary lesions and diabetes. TREM1 may also be helpful in predicting the 6-month MACEs after AMI.
Ji et al. (2021) Accuracy of triggering receptor expressed on myeloid cells 1 in diagnosis and prognosis of acute myocardial infarction: a prospective cohort study. PeerJ 9:e11655 https://doi.org/10.7717/peerj.11655
Similar seed dispersal systems by local frugivorous birds in native and alien plant species in a coastal seawall forest
Frugivorous birds play an important role in seed dispersal. Alien plant species’ seeds are dispersed by local birds in order to establish populations in new habitats. Alien plant species that produce fruits similar to that of native species have the potential to attract local birds, creating new mutualistic systems that are similar to the local ones. In autumn 2018 and 2019, we studied the seed dispersal systems of an alien plant species, Phytolacca americana, and a native species, Cayratia japonica, in a coastal seawall forest. Both plant species’ fruit, frugivorous bird foraging behaviors, seed germination rates, and seedling microhabitats were examined to determine whether the alien species had a similar seed dispersal system to that of the native species. Our results showed that P. americana and C. japonica had similar fruit type, color, and ripening period. There was a positive correlation between the percentage rate of fruit ripening and the percentage rate of fruit missing for both plant species, indicating that local frugivorous birds have the potential to sufficiently disperse the alien seeds to enable its spread in the coastal seawall forest (simple linear regression, P. americana: β = 0.863 ± 0.017, R2adj = 0.978, P < 0.01; C. japonica: β = 0.787 ± 0.034, R2adj = 0.898, P < 0.01). Eleven bird species consumed the fruits of the alien species or native species during the study period. Similar results were shown across alien and native species in bird foraging behavior (feeding frequency, feeding duration and first stop distance) indicating that a similar seed dispersal relationship had been established between local frugivorous and both plant species. The alien plant had a higher number of fruits carried by birds, suggesting that P. americana had a slightly higher fruit consumption than that of C. japonica (t-test, P < 0.01). Alien plant seedlings grow more abundant in forest gap microhabitat (t-test, P < 0.01). Our results confirmed that bird digestion promotes seed germination success in both plant species. Our study suggests that in a narrow coastal seawall forest, alien plant species can successfully establish their populations by relying on similar seed dispersal systems as the local species.
Liu et al. (2021) Similar seed dispersal systems by local frugivorous birds in native and alien plant species in a coastal seawall forest. PeerJ 9:e11672 https://doi.org/10.7717/peerj.11672