Novel rapid identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by real-time RT-PCR using BD Max Open System in Taiwan
Coronavirus disease 2019 has become a worldwide pandemic. By April 7, 2020, approximately 1,279,722 confirmed cases were reported worldwide including those in Asia, European Region, African Region and Region of the Americas. Rapid and accurate detection of Severe Acute Respiratory Syndrome Virus 2 (SARS-CoV-2) is critical for patient care and implementing public health measures to control the spread of infection. In this study, we developed and validated a rapid total nucleic acid extraction method based on real‐time RT-PCR for reliable, high‐throughput identification of SARS-CoV-2 using the BD MAX platform. For clinical validation, 300 throat swab and 100 sputum clinical samples were examined by both the BD MAX platform and in-house real-time RT-PCR methods, which showed 100% concordant results. This BD MAX protocol is fully automated and the turnaround time from sample to results is approximately 2.5 h for 24 samples compared to 4.8 h by in-house real-time RT-PCR. Our developed BD MAX RT-PCR assay can accurately identify SARS-CoV-2 infection and shorten the turnaround time to increase the effectiveness of control and prevention measures for this emerging infectious disease.
Perng et al. (2020) Novel rapid identification of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by real-time RT-PCR using BD Max Open System in Taiwan. PeerJ 8:e9318 https://doi.org/10.7717/peerj.9318
Contribution of prokaryotes and eukaryotes to CO2 emissions in the wastewater treatment process
Reduction of the greenhouse effect is primarily associated with the reduction of greenhouse gas (GHG) emissions. Carbon dioxide (CO2) is one of the gases that increases the greenhouse effect - it is responsible for about half of the greenhouse effect. Significant sources of CO2 are wastewater treatment plants (WWTPs) and waste management, with about 3% contribution to global emissions. CO2 is produced mainly in the aerobic stage of wastewater purification and is a consequence of activated sludge activity. Although the roles of activated sludge components in the purification process have been studied quite well, their quantitative contribution to CO2 emissions is still unknown. The emission of CO2 caused by prokaryotes and eukaryotes over the course of a year (taking into account subsequent seasons) in model sequencing batch reactors (SBR) is presented in this study. In this work, for the first time, we aimed to quantify this contribution of eukaryotic organisms to total CO2 emissions during the WWTP process. It is of the order of several or more ppm. The contribution of CO2 produced by different components of activated sludge in WWTPs can improve estimation of the emissions of GHGs in this area of human activity.
Jaromin-Gleń et al. (2020) Contribution of prokaryotes and eukaryotes to CO2 emissions in the wastewater treatment process. PeerJ 8:e9325 https://doi.org/10.7717/peerj.9325
Factors promoting the natural regeneration of Larix principis-rupprechtii plantation in the Lvliang Mountains of central China
Given their complexity, targeted care and management of different areas and tree species are necessary for enhancing the natural regeneration of forests. Thus, an understanding of changes in the overstory and understory is essential for ensuring successful regeneration. Promoting the natural regeneration of Larix principis-rupprechtii plantations is considered challenging; indeed, regional sustainable development through natural regeneration of many stands has often been considered unattainable. Here, we studied several plots with varying extents of regeneration to identify the most important factors that affect regeneration. The plots were divided into three forest types based on the number of regenerating plants. For each type of plot, we measured various factors that might potentially affect regeneration. Representational difference analysis was used to identify the most important factors >9% contribution). Based on these factors, multiple corrections were made to construct a structural equation model of topography, stand structure, soil properties and litter to identify the most important factors driving variation in regeneration. Positive correlations were detected between regeneration with diameter at breast height (0.21) and litter thickness (0.57). Regeneration was negatively correlated with soil (−0.54) and slope (−0.48). Additionally, the number of regenerating plants and the height of regenerating plants were strongly positively correlated. However, there was no significant relationship between regeneration and litter accumulation, stand density, altitude, average tree height, total P and total N. Overall, our study showed that key factors for promoting natural regeneration include appropriate litter thickness, strong parent trees, a gentle slope and sufficient quantities of soil nutrients. Moreover, our findings provide a reference for the design of effective management and restoration plans.
Liang et al. (2020) Factors promoting the natural regeneration of Larix principis-rupprechtii plantation in the Lvliang Mountains of central China. PeerJ 8:e9339 https://doi.org/10.7717/peerj.9339
Isolation, diversity, and antimicrobial activity of fungal endophytes from Rohdea chinensis (Baker) N.Tanaka (synonym Tupistra chinensis Baker) of Qinling Mountains, China
Endophytic fungi have been emerged as fruitful resources for producing structurally fascinating and biologically active secondary metabolites. However, endophytic fungi from medicinal plants of Qinling Mountains–the most important natural climatic boundary between the subtropical and warm temperate zones of China with an astonishingly high level of biodiversity–have rarely been explored as potential sources of novel fungal species and active secondary metabolites. In this study, a total of 371 fungal colonies were successfully isolated from 510 tissue segments of the medicinal Tupistra chinensis Baker collected from Qinling Mountains, China. Roots of T. chinensis Baker are used as a folk medicine to ameliorate pharyngitis and treat rheumatic diseases. A total of 100 representative morphotype strains were identified according to ITS rDNA sequence analyses and were grouped into three phyla (Ascomycota, Basidiomycota, Mucoromycota), seven classes (Dothideomycetes, Sordariomycetes, Eurotiomycetes, Microbotryomycetes, Agaricomycetes, Leotiomycetes, Mortierellomycetes), and at least 35 genera. The genera of Collectotrichum (IF, 29.92%), Fusarium (IF, 8.36%), Aspergillus (IF, 8.09%), and Dactylonectria (IF, 5.39%) were most frequently isolated from the tissues of T. chinensis Baker. The Species Richness Index (S, 65) and the Shannon-Wiener Index (H′, 3.7914) indicated that T. chinensis Baker harbored abundant fungal resources. Moreover, five isolates were potential new taxa because of low similarity of ITS sequences ranged from 95.09%∼96.61%. Fifteen out of 100 endophytic fungal ethyl acetate extracts exhibited inhibitory activities against at least one pathogenic bacterium or fungus. Two important lead compounds produced by two stains (F8047 and F8075) with high antimicrobial activities were identified using high performance liquid chromatography (HPLC) and ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC–QTOF MS) analyses. In addition, it was noteworthy that the strain F8001, which may be a potential new species, showed antimicrobial activity and should be investigated further. Overall, these results indicated that the endophytic fungi from T. chinensis Baker could be exploited as a novel source of bioactive compounds.
An et al. (2020) Isolation, diversity, and antimicrobial activity of fungal endophytes from Rohdea chinensis (Baker) N.Tanaka (synonym Tupistra chinensis Baker) of Qinling Mountains, China. PeerJ 8:e9342 https://doi.org/10.7717/peerj.9342
Identification of candidate genes and prognostic value analysis in patients with PDL1-positive and PDL1-negative lung adenocarcinoma
Background Increasing bodies of evidence reveal that targeting a programmed cell death protein 1 (PD-1) monoclonal antibody is a promising immunotherapy for lung adenocarcinoma. Although PD receptor ligand 1 (PDL1) expression is widely recognized as the most powerful predictive biomarker for anti-PD-1 therapy, its regulatory mechanisms in lung adenocarcinoma remain unclear. Therefore, we conducted this study to explore differentially expressed genes (DEGs) and elucidate the regulatory mechanism of PDL1 in lung adenocarcinoma. Methods The GSE99995 data set was obtained from the Gene Expression Omnibus (GEO) database. Patients with and without PDL1 expression were divided into PDL1-positive and PDL1-negative groups, respectively. DEGs were screened using R. The Gene Ontology (GO) database and Kyoto Encyclopedia of Genes and Genomes (KEGG) were analyzed using the Database for Annotation, Visualization and Integrated Discovery. Protein–protein interaction (PPI) networks of DEGs was visualized using Cytoscape, and the MNC algorithm was applied to screen hub genes. A survival analysis involving Gene Expression Profiling Interactive Analysis was used to verify the GEO results. Mutation characteristics of the hub genes were further analyzed in a combined study of five datasets in The Cancer Genome Atlas (TCGA) database. Results In total, 869 DEGs were identified, 387 in the PDL1-positive group and 482 in the PDL1-negative group. GO and KEGG analysis results of the PDL1-positive group mainly exhibited enrichment of biological processes and pathways related to cell adhesion and the peroxisome proliferators-activated receptors (PPAR) signaling pathway, whereas biological process and pathways associated with cell division and repair were mainly enriched in the PDL1-negative group. The top 10 hub genes were screened during the PPI network analysis. Notably, survival analysis revealed BRCA1, mainly involved in cell cycle and DNA damage responses, to be a novel prognostic indicator in lung adenocarcinoma. Moreover, the prognosis of patients with different forms of lung adenocarcinoma was associated with differences in mutations and pathways in potential hub genes. Conclusions PDL1-positive lung adenocarcinoma and PDL1-negative lung adenocarcinoma might be different subtypes of lung adenocarcinoma. The hub genes might play an important role in PDL1 regulatory pathways. Further studies on hub genes are warranted to reveal new mechanisms underlying the regulation of PDL1 expression. These results are crucial for understanding and applying precision immunotherapy for lung adenocarcinoma.
Qi et al. (2020) Identification of candidate genes and prognostic value analysis in patients with PDL1-positive and PDL1-negative lung adenocarcinoma. PeerJ 8:e9362 https://doi.org/10.7717/peerj.9362
Near-infrared-light pre-treatment attenuates noise-induced hearing loss in mice
Noise induced hearing loss (NIHL) is accompanied by a reduction of cochlear hair cells and spiral ganglion neurons. Different approaches have been applied to prevent noise induced apoptosis / necrosis. Physical intervention is one technique currently under investigation. Specific wavelengths within the near-infrared light (NIR)-spectrum are known to influence cytochrome-c-oxidase activity, which leads in turn to a decrease in apoptotic mechanisms. It has been shown recently that NIR can significantly decrease the cochlear hair cell loss if applied daily for 12 days after a noise exposure. However, it is still unclear if a single NIR-treatment, just before a noise exposure, could induce similar protective effects. Therefore, the present study was conducted to investigate the effect of a single NIR-pre-treatment aimed at preventing or limiting NIHL. The cochleae of adult NMRI-mice were pre-treated with NIR-light (808 nm, 120 mW) for 5, 10, 20, 30 or 40 minutes via the external ear canal. All animals were noised exposed immediately after the pre-treatment by broad band noise (5–20 kHz) for 30 minutes at 115 dB SPL. Frequency specific ABR-recordings to determine auditory threshold shift were carried out before the pre-treatment and two weeks after the noise exposure. The amplitude increase for wave IV and cochlear hair cell loss were determined. A further group of similar mice was noise exposed only and served as a control for the NIR pre-exposed groups. Two weeks after noise exposure, the ABR threshold shifts of NIR-treated animals were significantly lower (p < 0.05) than those of the control animals. The significance was at three frequencies for the 5-minute pre-treatment group and across the entire frequency range for all other treatment groups. Due to NIR light, the amplitude of wave four deteriorates significantly less after noise exposure than in controls. The NIR pre-treatment had no effect on the loss of outer hair cells, which was just as high with or without NIR-light pre-exposure. Relative to the entire number of outer hair cells across the whole cochlea, outer hair cell loss was rather negligible. No inner hair cell loss whatever was detected. Our results suggest that a single NIR pre-treatment induces a very effective protection of cochlear structures from noise exposure. Pre-exposure of 10 min seems to emerge as the optimal dosage for our experimental setup. A saturated effect occurred with higher dosage-treatments. These results are relevant for protection of residual hearing in otoneurosurgery such as cochlear implantation.
Basta et al. (2020) Near-infrared-light pre-treatment attenuates noise-induced hearing loss in mice. PeerJ 8:e9384 https://doi.org/10.7717/peerj.9384
Identification of SPRR3 as a novel diagnostic/prognostic biomarker for oral squamous cell carcinoma via RNA sequencing and bioinformatic analyses
Oral squamous cell carcinoma (OSCC) has always been one of the most aggressive and invasive cancers among oral and maxillofacial malignancies. As the morbidity and mortality of the disease have increased year by year, the search for a promising diagnostic and prognostic biomarker for the disease is becoming increasingly urgent. Tumorous and adjacent tissues were collected from three OSCC sufferers and we obtained 229 differentially expressed genes (DEGs) between tumor and normal tissues via high-throughput RNA sequence. Function and pathway enrichment analyses for DEGs were conducted to find a correlation between tumorigenesis status and DEGs. Protein interaction network and molecular complex detection (MCODE) were constructed to detect core modules. Two modules were enriched in MCODE. The diagnostic and prognostic values of the candidate genes were analyzed, which provided evidence for the candidate genes as new tumor markers. Small Proline Rich Protein 3 (SPRR3), a potential tumor marker that may be useful for the diagnosis of OSCC, was screened out. The survival analysis showed that SPRR3 under expression predicted the poor prognosis of OSCC patients. Further experiments have also shown that the expression of SPRR3 decreased as the malignancy of OSCC increased. Therefore, we believe that SPRR3 could be used as a novel diagnostic and prognostic tumor marker.
Yu et al. (2020) Identification of SPRR3 as a novel diagnostic/prognostic biomarker for oral squamous cell carcinoma via RNA sequencing and bioinformatic analyses. PeerJ 8:e9393 https://doi.org/10.7717/peerj.9393
CRISPR 2 PCR and high resolution melting profiling for identification and characterization of clinically-relevant Salmonella enterica subsp. enterica
Background Nontyphoidal Salmonella spp. constitute a major bacterial cause of food poisoning. Each Salmonella serotype causes distinct virulence to humans. Method A small cohort study was conducted to characterize several aspects of Salmonella isolates obtained from stool of diarrheal patients (n = 26) admitted to Phayao Ram Hospital, Phayao province, Thailand. A simple CRISPR 2 molecular analysis was developed to rapidly type Salmonella isolates employing both uniplex and high resolution melting (HRM) curve analysis. Results CRISPR 2 monoplex PCR generated a single Salmonella serotype-specific amplicon, showing S. 4,[5],12:i:- with highest frequency (42%), S. Enteritidis (15%) and S. Stanley (11%); S. Typhimurium was not detected. CRISPR 2 HRM-PCR allowed further classification of S. 4,[5],12:i:- isolates based on their specific CRISPR 2 signature sequences. The highest prevalence of Salmonella infection was during the summer season (April to August). Additional studies were conducted using standard multiplex HRM-PCR typing, which confirmed CRISPR 2 PCR results and, using a machine-learning algorithm, clustered the majority of Salmonella serotypes into six clades; repetitive element-based (ERIC) PCR, which clustered the serotypes into three clades only; antibiogram profiling, which revealed the majority resistant to ampicillin (69%); and test for extended spectrum β-lactamase production (two isolates) and PCR-based detection of bla alleles. Conclusion CRISPR 2 PCR provided a simple assay for detection and identification of clinically-relevant Salmonella serotypes. In conjunction with antibiogram profiling and rapid assay for β-lactamase producers, this approach should facilitate detection and appropriate treatment of Salmonellosis in a local hospital setting. In addition, CRISPR 2 HRM-PCR profiling enabled clustering of S. 4,[5],12:i:-isolates according to CRISPR 2 locus signature sequences, indicative of their different evolutionary trajectories, thereby providing a powerful tool for future epidemiological studies of virulent Salmonella serotypes.
Wisittipanit et al. (2020) CRISPR 2 PCR and high resolution melting profiling for identification and characterization of clinically-relevant Salmonella enterica subsp. enterica. PeerJ 8:e9113 https://doi.org/10.7717/peerj.9113
Quality of life after hip fracture: a 12-month prospective study
Background Hip fracture is an important and frequent health problem worldwide. To date, there are still limited studies focused on the analysis of health-related quality of life (HRQOL) after a hip fracture in the Spanish population, especially with long-term follow-up. Objective To determine the HRQOL at 12 months after hip fracture and to identify potential factors associated with HRQOL. Design Prospective observational study. Setting Traumatology units of two university hospitals in province Cáceres (Spain). Participants A total of 224 patients were admitted to the unit and required immediate surgery due to a hip fracture. Methods HRQOL was measured with the EuroQol-5D questionnaire (EQ-5D) and the SF-12 Health Survey. Results Scores from the visual analog scale EQ-5D decreased significantly (p < 0.001) from 72.8 at baseline to 48.3 after 1 month, to 48.2 after 6 months and to 46.1 after 12 months. The EQ-5D index score showed a similar significant reduction (p < 0.001) from 0.6 to 0.1, 0.3 and 0.3, respectively. Values of the physical component summary (PCS-12) significantly decreased (p < 0.001) from 38.6 at baseline to 31.0, 33.1 and 33.5. The mental component summary (MCS-12) decreased from 46.5 to 44.8 after 6 months (p = 0.022) and 44.3 after 12 months (p = 0.005). Factors potentially associated with HRQOL at 12 months after hip fracture were depression status after 12 months (B = 0–1.876; 95% CI [−2.409 to −1.343]; p < 0.001), functional ambulation classification after 12 months (B = −12.133; 95% CI [−17.970 to −6.297]; p < 0.001), EQ-5D VAS at baseline (B = 0.223; 95% CI [0.115–0.330]; p < 0.001), and age (B = −0.323; 95% CI [−0.594 to −0.053; p = 0.015). Conclusions Patients experience a significant impairment in HRQOL H after a hip fracture, especially in self-care, pain/discomfort, usual activities, mobility and anxiety/depression. The decline in the HRQOL is effective the first month and lasts at least 12 months after the surgical intervention.
Amarilla-Donoso et al. (2020) Quality of life after hip fracture: a 12-month prospective study. PeerJ 8:e9215 https://doi.org/10.7717/peerj.9215
Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils
Background Vulnerable species experiencing inbreeding depression are prone to localised extinctions because of their reduced fitness. For Tasmanian devils, the rapid spread of devil facial tumour disease (DFTD) has led to population declines and fragmentation across the species’ range. Here we show that one of the few remaining DFTD-free populations of Tasmanian devils is experiencing inbreeding depression. Moreover, this population has experienced a significant reduction in reproductive success over recent years. Methods We used 32 microsatellite loci to examine changes in genetic diversity and inbreeding in the wild population at Woolnorth, alongside field data on breeding success from females to test for inbreeding depression. Results Wefound that maternal internal relatedness has a negative impact on litter sizes. The results of this study imply that this population may be entering an extinction vortex and that to protect the population genetic rescue should be considered. This study provides conservation managers with useful information for managing wild devils and provides support for the “Wild Devil Recovery Program”, which is currently augmenting small, isolated populations.
Gooley et al. (2020) Inbreeding depression in one of the last DFTD-free wild populations of Tasmanian devils. PeerJ 8:e9220 https://doi.org/10.7717/peerj.9220