Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2
Background Highly sensitive real-time reverse transcription polymerase chain reaction (RT-qPCR) methods have been developed for the detection of SARS-CoV-2. However, they are costly. Loop-mediated isothermal amplification (LAMP) assay has emerged as a novel alternative isothermal amplification method for the detection of nucleic acid. Methods A rapid, sensitive and specific real-time reverse transcription LAMP (RT-LAMP) assay was developed for SARS-CoV-2 detection. Results This assay detected one copy/reaction of SARS-CoV-2 RNA in 30 min. Both the clinical sensitivity and specificity of this assay were 100%. The RT-LAMP showed comparable performance with RT-qPCR. Combining simplicity and cost-effectiveness, this assay is therefore recommended for use in resource resource-limited settings.
Lau et al. (2020) Real-time reverse transcription loop-mediated isothermal amplification for rapid detection of SARS-CoV-2. PeerJ 8:e9278 https://doi.org/10.7717/peerj.9278
Ginsenoside panaxatriol reverses TNBC paclitaxel resistance by inhibiting the IRAK1/NF-κB and ERK pathways
Background Paclitaxel (PTX) resistance is a major obstacle in the treatment of triple-negative breast cancer (TNBC). Previously, we have reported that interleukin-1 receptor-associated kinase 1 (IRAK1) and its downstream pathways are associated with PTX resistance in TNBC cells. In this study, we sought to investigate the combination treatment of ginsenoside panaxatriol (GPT), one of the main active components in Panax ginseng, with PTX on viability and apoptosis of TNBC PTX resistant cells, and explore the role of IRAK1 mediated signaling pathways in the therapeutic effects. Methods CellTiter-Glo and colony formation assays were used to assess cell viability. Flow cytometry was used to analyze subG1 and apoptosis. Western blot was used to detect expressions of proteins involved in apoptosis and the IRAK1/NF-κB and ERK pathways. The mRNA expression of inflammatory cytokines, S100A7/8/9 and cancer stem cell (CSC)-related genes were examined by qPCR. Stem cells were identified by tumor sphere assay. Cell invasion ability was examined by transwell assay. Results We show that GPT inhibits MDA-MB-231 PTX resistant (MB231-PR) cell viability in a dose-dependent manner. When combined with PTX, GPT synergistically causes more cell death, induces subG1 accumulation and cell apoptosis. Besides, up-regulation of BAX/BCL-2 ratio, and down-regulation of MCL-1 are also observed. Moreover, this combination inhibits IRAK1, NF-κB and ERK1/2 activation, and leads to down-regulation of inflammatory cytokines (IL6, IL8, CXCL1, CCL2), S100A7/9 and CSC-related genes (OCT4, SOX2, NANOG, ALDH1, CD44) expression. In addition, the combination treatment suppresses MB231-PR cell invasion ability, and impairs tumor sphere growth both in MB231-PR and SUM159 PTX resistant (SUM159-PR) cells. Conclusion Our study demonstrates that GPT can resensitize TNBC PTX resistant cells to PTX by inhibiting the IRAK1/NF-κB and ERK pathways and reducing stem cell characteristics.
Wang et al. (2020) Ginsenoside panaxatriol reverses TNBC paclitaxel resistance by inhibiting the IRAK1/NF-κB and ERK pathways. PeerJ 8:e9281 https://doi.org/10.7717/peerj.9281
Association of FKBP5 polymorphisms with patient susceptibility to coronary artery disease comorbid with depression
Background Coronary artery disease (CAD) and depression cause great burden to society and frequently co-occur. The exact mechanisms of this comorbidity are unclear. FK506-binding protein 51 (FKBP51) is correlated with cardiovascular disease and depression. The aim of this study was to determine the role of the seven single nucleotide polymorphisms (SNPs) of FKBP5 that code FKBP51, namely, rs1360780 (C>T), rs2817032 (T>C), rs2817035 (G>A), rs9296158 (G>A), rs9470079 (G>A), rs4713902 (T>C), and rs3800373 (C>T) in a patient’s susceptibility to comorbid CAD and depression. Methods We enrolled 271 Northern Chinese Han patients with CAD, including 123 patients with depression and 147 patients without depression. We also included 113 healthy controls that match the patients’ sex and age. Genomic DNA from whole blood was extracted, and seven SNPs were assessed using MassArray method. Patient Health Questionnaire-9 was applied to access the depression. Results The GA genotype for rs9470079 was associated with a significantly decreased risk of CAD (odds ratio = 0.506, 95% confidence interval = 0.316–0.810, P = 0.005) when the GG genotype was used as reference. A statistically significant difference was observed among females but not among males in the rs9470079 genotype and allele frequency. Patients with CAD were further divided into CAD+D and CAD-D groups according to the presence of comorbid depression and were compared with the controls. Significant differences were found regarding the genotype and allele frequency of rs2817035 and rs9470079 in CAD+H groups compared with the control subjects in all groups and the female groups (P < 0.05). Conclusions The current study found a remarkable association between FKBP5 gene variations and the risk of comorbid CAD and depression in a north Chinese population. rs9470079 may be a potential gene locus for the incidence of comorbid CAD and depression.
Wang et al. (2020) Association of FKBP5 polymorphisms with patient susceptibility to coronary artery disease comorbid with depression. PeerJ 8:e9286 https://doi.org/10.7717/peerj.9286
The effect of journal guidelines on the reporting of antibody validation
Background Despite the widespread use of antibodies as a research tool, problems with specificity, lot-to-lot consistency and sensitivity commonly occur and may be important contributing factors to the ‘replication crisis’ in biomedical research. This makes the validation of antibodies and accurate reporting of this validation in the scientific literature extremely important. Therefore, some journals now require authors to comply with antibody reporting guidelines. Methods We used a quasi-experimental approach to assess the effectiveness of such journal guidelines in improving antibody reporting in the scientific literature. In a sample of 120 publications, we compared the reporting of antibody validation and identification information in two journals with guidelines (Nature and the Journal of Comparative Neurology) with two journals without guidelines (Science and Neuroscience), before and after the introduction of these guidelines. Results Our results suggest that the implementation of antibody reporting guidelines might have some influence on the reporting of antibody validation information. The percentage of validated antibodies per article slightly increased from 39% to 57% in journals with guidelines, whereas this percentage decreased from 23% to 14% in journals without guidelines. Furthermore, the reporting of validation information of all primary antibodies increased by 23 percentage points in the journals with guidelines (OR = 2.80, 95% CI = 0.96-INF; adjusted p = 1, one-tailed), compared to a decrease of 13 percentage points in journals without guidelines. Fortunately, the guidelines seem to be more effective in improving the reporting of antibody identification information. The reporting of identification information of all primary antibodies used in a study increased by 58 percentage points (OR = 17.8, 95% CI = 4.8-INF; adjusted p = 0.0003, one-tailed) in journals with guidelines. This percentage also slightly increased in journals without guidelines (by 18 percentage points), suggesting an overall increased awareness of the importance of antibody identifiability. Moreover, this suggests that reporting guidelines mostly have an influence on the reporting of information that is relatively easy to provide. A small increase in the reporting of validation by referencing the scientific literature or the manufacturer’s data also indicates this. Conclusion Combined with the results of previous studies on journal guidelines, our study suggests that the effect of journal antibody guidelines on validation practices by themselves may be limited, since they mostly seem to improve antibody identification instead of actual experimental validation. These guidelines, therefore, may require additional measures to ensure effective implementation. However, due to the explorative nature of our study and our small sample size, we must remain cautious towards other factors that might have played a role in the observed change in antibody reporting behaviour.
Hoek et al. (2020) The effect of journal guidelines on the reporting of antibody validation. PeerJ 8:e9300 https://doi.org/10.7717/peerj.9300
Air transportation, population density and temperature predict the spread of COVID-19 in Brazil
There is evidence that COVID-19, the disease caused by the betacoronavirus SARS-CoV-2, is sensitive to environmental conditions. However, such conditions often correlate with demographic and socioeconomic factors at larger spatial extents, which could confound this inference. We evaluated the effect of meteorological conditions (temperature, solar radiation, air humidity and precipitation) on 292 daily records of cumulative number of confirmed COVID-19 cases across the 27 Brazilian capital cities during the 1st month of the outbreak, while controlling for an indicator of the number of tests, the number of arriving flights, population density, proportion of elderly people and average income. Apart from increasing with time, the number of confirmed cases was mainly related to the number of arriving flights and population density, increasing with both factors. However, after accounting for these effects, the disease was shown to be temperature sensitive: there were more cases in colder cities and days, and cases accumulated faster at lower temperatures. Our best estimate indicates that a 1 °C increase in temperature has been associated with a decrease in confirmed cases of 8%. The quality of the data and unknowns limit the analysis, but the study reveals an urgent need to understand more about the environmental sensitivity of the disease to predict demands on health services in different regions and seasons.
Pequeno et al. (2020) Air transportation, population density and temperature predict the spread of COVID-19 in Brazil. PeerJ 8:e9322 https://doi.org/10.7717/peerj.9322
Monitoring of UN sustainable development goal SDG-9.1.1: study of Algerian “Belt and Road” expressways constructed by China
The proportion of the rural population who live within 2 km of an all-season road is an indicator of the United Nations’ Sustainable Development Goals (SDGs) 9.1.1. This paper aims to calculate SDG indicator 9.1.1 in the proximity of five Algerian expressways. Three monitoring methods are proposed for different spatial regions based on the five expressways built by China’s Belt and Road Initiative Project. These methods are based on remote sensing and WorldPop and The High Resolution Settlement Layer (HRSL) population data. The results indicate that (1) the WorldPop population statistics show that the five expressways built by China’s Belt Project have increased the rural population of the 2 km buffer zone by 192,016 between the start of construction and eight years after its completion. By the end of 2019, the population increased by 329,291 accounting for 1.17% of the rural population. (2) Based on populations estimated form built-up index (NDBI) building areas, the rural populations within the 2 km buffer area of the Bejaia-Haniff Expressway in 2011, 2015, and 2019 were 273,118, 306,430, and 375,408, respectively. (3) HRSL population grid statistics indicate that, in 2015, the populations were: East-West Expressway = 911,549, Bejaia Expressway = 127,471, Tipaza Expressway = 71,411, North-South Expressway = 30,583, and Cherchell Ring Expressway = 41,657. (4) A visual interpretation method based on Google Earth imagery was used to count the number of buildings and number of building floors in the town of Tikhramtath. Based on the estimated population of each building and floor, the population of Tikhramtath town in 2011, 2015, 2017, and 2019 was estimated as 1,790, 2,785, 3,365, and 3,870, respectively. (5) Through analysis and accuracy assessment, the appropriate statistical methods for different regions were determined.
Spatial and Geographic Information Science
Jia et al. (2020) Monitoring of UN sustainable development goal SDG-9.1.1: study of Algerian “Belt and Road” expressways constructed by China. PeerJ 8:e8953 https://doi.org/10.7717/peerj.8953
Phyllosphere bacterial assembly in citrus crop under conventional and ecological management
Divergences between agricultural management can result in different types of biological interactions between plants and microorganisms, which may affect food quality and productivity. Conventional practices are well-established in the agroindustry as very efficient and lucrative; however, the increasing demand for sustainable alternatives has turned attention towards agroecological approaches. Here we intend to explore microbial dynamics according to the agricultural management used, based on the composition and structure of these bacterial communities on the most environmentally exposed habitat, the phyllosphere. Leaf samples were collected from a Citrus crop (cultivated Orange) in Mogi-Guaçu (SP, Brazil), where either conventional or ecological management systems were properly applied in two different areas. NGS sequencing analysis and quantitative PCR allowed us to comprehend the phyllosphere behavior and µ-XRF (micro X-ray fluorescence) could provide an insight on agrochemical persistence on foliar tissues. Our results demonstrate that there is considerable variation in the phyllosphere community due to the management practices used in the citrus orchard, and it was possible to quantify most of this variation. Equally, high copper concentrations may have influenced bacterial abundance, having a relevant impact on the differences observed. Moreover, we highlight the intricate relationship microorganisms have with crop production, and presumably with crop yield as well.
Carvalho et al. (2020) Phyllosphere bacterial assembly in citrus crop under conventional and ecological management. PeerJ 8:e9152 https://doi.org/10.7717/peerj.9152
Limpet disturbance effects on barnacle recruitment are related to recruitment intensity but not recruit size
Intertidal limpets are important grazers along rocky coastlines worldwide that not only control algae but also influence invertebrates such as common barnacles. For instance, grazing limpets ingest settling barnacle cyprid larvae (hereafter cyprids) and push cyprids and barnacle recruits off the substrate. Such limpet disturbance effects (LDEs) can limit barnacle recruitment, a key demographic variable affecting barnacle population establishment and persistence. In this study, we examined limpet (Lottia cassis) disturbance to barnacle (Chthamalus dalli, Balanus glandula) recruitment on the Pacific coast of Hokkaido, Japan, as information on limpet-barnacle interactions from this region is missing. We investigated, for the first time, whether barnacle size and recruitment intensity influence LDEs on barnacle recruitment. Small barnacles may be less susceptible to LDEs than larger barnacles, because small size may reduce the propbability of limpet disturbance. Moreover, recruitment intensity can influence LDEs, as high recruitment can compensate for LDEs on barnacle recruitment density. In Hokkaido, C. dalli cyprids are smaller than B. glandula cyprids, and C. dalli recruitment is higher than B. glandula recruitment. Thus, we hypothesized that LDEs on C. dalli recruitment would be weaker than those on B. glandula recruitment. To test our hypothesis, we conducted a field experiment during which we manipulated limpet presence/absence on the interior surfaces of ring-shaped cages. After four weeks, we measured barnacle recruitment and recruit size on the interior surfaces of the cages and found negative LDEs on C. dalli and B. glandula recruitment and recruit size. As hypothesized, the LDEs on C. dalli recruitment were weaker than the LDEs on B. glandula recruitment. Additionally, C. dalli recruits were smaller than B. glandula recruits. However, the LDEs on C. dalli recruit size were as strong as the LDEs on B. glandula recruit size, indicating that the smaller C. dalli recruits are not less susceptible to LDEs than B. glandula recruits. Since C. dalli recruitment was higher than B. glandula recruitment, we propose that the higher C. dalli recruitment compensated for the LDEs on C. dalli recruitment. Our findings indicate that the detected differences in LDEs on barnacle recruitment are related to barnacle recruitment intensity but not recruit size.
Ellrich et al. (2020) Limpet disturbance effects on barnacle recruitment are related to recruitment intensity but not recruit size. PeerJ 8:e9190 https://doi.org/10.7717/peerj.9190
Repurposing a traditional Japanese method of pest control for wintering pine moths, Komo-trap, for use against summer and winter populations of fall webworms
Background The fall webworm, Hyphantria cunea Drury (Lepidoptera: Erebidae), is a widespread invasive species. It is native to North America, ranging from southern Canada to northern Mexico. During and after the 1940s, this pest was accidentally introduced in many parts of Europe and Asia. It has now spread to more than 30 countries. The larvae feed on leaves of a wide range of tree species, including ones used as street trees in cities, causing an increase in urban management cost. Although several pest management methods have been employed, pest damage continues especially in newly invaded areas. In this study, we examined the effect and cost-effectiveness of the komo-trap, traditionally used in Japan to reduce the population of larvae of the pine moth Dendrolimus spectabilis Butler (Lepidoptera: Lasiocampidae). This trap, which is safe for people and ecosystems, has not yet been applied to trap the fall webworm. Methods In two seasons of 2017, we set komo-traps on street trees in Hakodate City, Japan. We counted the numbers of captured fall webworms compared with controls. We also monitored other species to evaluate any nontarget effects of the trap. Results One komo, the material cost of which is about 1.10 USD, captured 43.8 fall webworms on average in summer and 27.2 in the fall. The values were significantly larger than those of the controls, which were 0.07 in summer and 0.14 in winter. Bycatch of other species was minimal in summer, whereas in the fall one komo, on average, caught 10.7 woodlice Porcellio sp. or spp. (Isopoda: Porcellionidae). Discussion The komo-trap is effective in capturing fall webworm. The cost performance of the trap is very favorable, and the nontarget effects can be reduced by using the trap in summer only. The komo-trap would complement other control methods such as tree pruning. Because its cost is low, we recommend that the komo-trap be introduced as a larger-scale trial.
Mikami et al. (2020) Repurposing a traditional Japanese method of pest control for wintering pine moths, Komo-trap, for use against summer and winter populations of fall webworms. PeerJ 8:e9244 https://doi.org/10.7717/peerj.9244
The severity of mobile phone addiction and its relationship with quality of life in Chinese university students
Objective This study examined the severity of mobile phone addiction and its relationship with quality of life (QOL) in Chinese university students. Methods A total of 2,312 university students from Macao, Hong Kong and mainland China participated in this cross-sectional study. The Mobile Phone Addiction Scale (MPAS), and the World Health Organization Quality of Life-Brief version (WHOQOL-BREF) rating instruments were used to assess the severity of mobile phone addiction and QOL, respectively. Results Compared to students in mainland China, those in Macao and Hong Kong were more likely to have excessive mobile phone use. Multiple linear regression revealed that high academic pressure and poor academic performance were positively associated, while male gender, greater interest in academic major and long sleep duration were negatively associated with the severity of mobile phone addiction. Students addicted to mobile phone use had significantly lower scores across all QOL domains. Conclusion Due to the adverse impact of excessive mobile phone use on QOL, public education and effective preventive measures should be developed for Chinese university students.
Li et al. (2020) The severity of mobile phone addiction and its relationship with quality of life in Chinese university students. PeerJ 8:e8859 https://doi.org/10.7717/peerj.8859