A novel one-step quick assay for detection of SARS-COV2 antibodies across mammalian species
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) has so far infected almost a hundred of millions of people and caused more than a million of death across the world. Many serological tests have been developed to track down virus infection in community via identification of antibodies against SARS-CoV2 virus. However, the tests vary in sensitivity, specificity, complexity, and speed. Here, I developed a simple, one-step, quick test to detect antibodies against SARS-CoV2 N (scN) nucleocapsid protein via direct visualization of antigen-antibody reaction. A total of 40 serum samples of SARS-CoV2 patients were purchased from RayBiotech. A total of 50 pre-pandemic human serum samples from San Diego Blood Bank were used as negative controls. After performing the one-step quick test of these 90 serum samples, I found that 39 samples are positive for anti-scN antibodies. All of the 39 positives are from the 40 SARS-CoV2 patients, suggesting that the one-step test is more sensitive than the lateral flow immunoassay (LFIA), the most widely used rapid antibody test. None of the 50 pre-pandemic samples is positive for anti-scN antibodies, indicating that the one-step test has an excellent specificity. The one-step test takes only ~5 min to detect the antibodies; and 1 ml of Escherichia coli culture can produce reagent proteins sufficient for thousands of the tests. Since the one-step test does not need a secondary antibody, it can be used as a universal test for anti-scN antibodies across different mammalian species to track down both human infection and the animal reservoir of SARS-CoV2 virus.
Zhou (2021) A novel one-step quick assay for detection of SARS-COV2 antibodies across mammalian species. PeerJ 9:e11381 https://doi.org/10.7717/peerj.11381
HiCEnterprise: identifying long range chromosomal contacts in Hi-C data
Motivation Computational analysis of chromosomal contact data is currently gaining popularity with the rapid advance in experimental techniques providing access to a growing body of data. An important problem in this area is the identification of long range contacts between distinct chromatin regions. Such loops were shown to exist at different scales, either mediating relatively short range interactions between enhancers and promoters or providing interactions between much larger, distant chromosome domains. A proper statistical analysis as well as availability to a wide research community are crucial in a tool for this task. Results We present HiCEnterprise, a first freely available software tool for identification of long range chromatin contacts not only between small regions, but also between chromosomal domains. It implements four different statistical tests for identification of significant contacts for user defined regions or domains as well as necessary functions for input, output and visualization of chromosome contacts. Availability The software and the corresponding documentation are available at: github.com/regulomics/HiCEnterprise. Supplementary information Supplemental data are available in the online version of the article and at the website regulomics.mimuw.edu.pl/wp/hicenterprise.
Kranas et al. (2021) HiCEnterprise: identifying long range chromosomal contacts in Hi-C data. PeerJ 9:e10558 https://doi.org/10.7717/peerj.10558
Recruitment of toxin-like proteins with ancestral venom function supports endoparasitic lifestyles of Myxozoa
Cnidarians are the oldest lineage of venomous animals and use nematocysts to discharge toxins. Whether venom toxins have been recruited to support parasitic lifestyles in the Endocnidozoa (Myxozoa + Polypodium) is, however, unknown. To examine this issue we variously employed transcriptomic, proteomic, associated molecular phylogenies, and localisation studies on representative primitive and derived myxozoans (Malacosporea and Myxosporea, respectively), Polypodium hydriforme, and the free-living staurozoan Calvadosia cruxmelitensis. Our transcriptomics and proteomics analyses provide evidence for expression and translation of venom toxin homologs in myxozoans. Phylogenetic placement of Kunitz type serine protease inhibitors and phospholipase A2 enzymes reveals modification of toxins inherited from ancestral free-living cnidarian toxins, and that venom diversity is reduced in myxozoans concordant with their reduced genome sizes. Various phylogenetic analyses of the Kunitz-type toxin family in Endocnidozoa suggested lineage-specific gene duplications, which offers a possible mechanism for enhancing toxin diversification. Toxin localisation in the malacosporean Buddenbrockia plumatellae substantiates toxin translation and thus illustrates a repurposing of toxin function for endoparasite development and interactions with hosts, rather than for prey capture or defence. Whether myxozoan venom candidates are expressed in transmission stages (e.g. in nematocysts or secretory vesicles) requires further investigation.
Hartigan et al. (2021) Recruitment of toxin-like proteins with ancestral venom function supports endoparasitic lifestyles of Myxozoa. PeerJ 9:e11208 https://doi.org/10.7717/peerj.11208
Hematological and cytochemical characteristics of peripheral blood cells in the argus snakehead (Ophiocephalus argus Cantor)
Background The argus snakehead (Ophiocephalus argus Cantor) is a highly nutritious, freshwater, cultured bony fish with a high economic value. The health of the fish is closely related to its blood cells, which are critical for oxygen transport, natural defense, and immunity. We investigated the morphometry, microstructure, and cytochemical characteristics of the peripheral blood cells of O. argus. Our results may provide the basic reference values needed to monitor the health of this fish for large-scale cultivation. Methods The number of blood cells in O. argus were counted on a hemocytometer and their size was measured using a micrometer under light microscope. The morphology and classification of the blood cells were studied using Wright’s staining and the cytochemical characteristics were studied using seven chemical stains including peroxidase (POX), Sudan black B (SBB), periodic acid-Schiff (PAS), acid phosphatase (ACP), alkaline phosphatase (ALP), chloroacetic acid AS-D naphthol esterase (AS-D), and α-naphthol acetate esterase (α-NAE). Results The peripheral blood cells in O. argus can be classified as erythrocytes, leukocytes, and thrombocytes; of which, females had 2.9597 million/mm3, 88,400/mm3, and 43,600/mm3, respectively, and males had 3.0105 million/mm3, 105,500/mm3, and 34,000/mm3, respectively. Leukocytes consisted of neutrophils, monocytes, large lymphocytes, and small lymphocytes. Eosinophils and basophils were not found. Monocytes were the most numerous leukocytes identified, followed by neutrophils and small lymphocytes, while large lymphocytes were the least frequently identified. Cytochemical staining showed that erythrocytes were only positive for PAS staining. Neutrophils were strongly positive for POX, SBB, and ACP, and positive for all the other cytochemical stains. Monocytes were positive for PAS and α-NAE and were weakly positive for ACP and AS-D staining. Large lymphocytes were positive for PAS and were weakly positive for ALP, AS-D, and α-NAE staining. Small lymphocytes were positive for PAS and weakly positive for AS-D and α-NAE staining. Thrombocytes were positive for PAS and were weakly positive for ACP and AS-D, but negative for the remaining cytochemical stains. The morphology of peripheral blood cells in O. argus was generally similar to that of other fish species, while the cytochemical staining patterns showed clear species specificity.
Wang et al. (2021) Hematological and cytochemical characteristics of peripheral blood cells in the argus snakehead (Ophiocephalus argus Cantor). PeerJ 9:e11234 https://doi.org/10.7717/peerj.11234
Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves
Background Vernonia amygdalina as a tropical horticultural crop has been widely used for medicinal herb, feed, and vegetable. Recently, increasing studies revealed that this species possesses multiple pharmacological properties. Notably, V. amygdalina leaves possess an abundance of flavonoids, but the specific profiles of flavonoids and the mechanisms of fl avonoid bi osynthesis in developing leaves are largely unknown. Methods The total flavonoids of V. amygdalina leaves were detected using ultraviolet spectrophotometer. The temporal flavonoid profiles of V. amygdalina leaves were analyzed by LC-MS. The transcriptome analysis of V. amygdalina leaves was performed by Illumina sequencing. Functional annotation and differential expression analysis of V. amygdalina genes were performed by Blast2GO v2.3.5 and RSEM v1.2.31, respectively. qRT-PCR analysis was used to verify the gene expressions in developing V. amygdalina leaves. Results By LC-MS analysis, three substrates (p-coumaric acid, trans-cinnamic acid, and phenylalanine) for flavonoid biosynthesis were identified in V. amygdalina leaves. Additionally, 42 flavonoids were identified from V. amygdalina leaves, including six dihydroflavones, 14 flavones, eight isoflavones, nine flavonols, two xanthones, one chalcone, one cyanidin, and one dihydroflavonol. Glycosylation and methylation were common at the hydroxy group of C3, C7, and C4’ positions. Moreover, dynamic patterns of different flavonoids showed diversity. By Illumina sequencing, the obtained over 200 million valid reads were assembled into 60,422 genes. Blast analysis indicated that 31,872 genes were annotated at least in one of public databases. Greatly increasing molecular resources makes up for the lack of gene information in V. amygdalina. By digital expression profiling and qRT-PCR, we specifically characterized some key enzymes, such as Va-PAL1, Va-PAL4, Va-C4H1, Va-4CL3, Va-ACC1, Va-CHS1, Va-CHI, Va-FNSII, and Va-IFS3, involved in flavonoid biosynthesis. Importantly, integrated metabolome and transcriptome data of V. amygdalina leaves, we systematically constructed a flavonoid biosynthetic pathway with regards to material supplying, flavonoid scaffold biosynthesis, and flavonoid modifications. Our findings contribute significantly to understand the underlying mechanisms of flavonoid biosynthesis in V. amygdalina leaves, and also provide valuable information for potential metabolic engineering.
Shui et al. (2021) Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves. PeerJ 9:e11239 https://doi.org/10.7717/peerj.11239
Experiencing fear during the pandemic: validation of the fear of COVID-19 scale in Polish
Background The Fear of COVID-19 Scale (FCV-19S) is a brief self-report measure developed at the beginning of the coronavirus pandemic. The scale evaluates the emotional responses to COVID-19. To date, the FCV-19S has been translated and validated in about 20 languages and has been used in many published research. The current study aimed to validate the Polish version of the FCV-19S. Method The FCV-19S was translated into Polish using forward- and back-translation. From May 15th to June 15th 2020, a total of 708 community members (Sample 1: 383 persons, 209 females, Sample 2: 325 persons, 198 females) participated in the online study. The participants were recruited using online advertisements in social media. Participation was anonymous, voluntary, and without compensation. A confirmatory factor analysis was performed to test the one-factor structure of the FCV-19S. Then, measurement invariance was analyzed across samples, gender and age groups. To assess the validity of the scale, correlations between the FCV-19S and the remaining scales were computed. Results Internal consistency of the FCV-19S was good in both samples (Cronbach’s alpha 0.89 and 0.85). The CFA showed that the one-factor model fits the data well (RMSEA = 0.067, 90% CI [0.059–0.094], CFI = 0.977, TLI = 0.965, GFI = 0.986). The criteria for configural, metric, scalar and strict invariance were met for all models tested. The FCV-19S scores correlated significantly with age, subjective vulnerability to the disease, neuroticism, self-reported compliance with the pandemic measures, and three kinds of preventive behavior (i.e., social distancing, hand hygiene, and disinfecting things). Conclusion The Polish version of the FCV-19S had a unidimensional structure, good reliability, and correlated as predicted with other variables. With the FCV-19S and the obtained results, healthcare professionals, researchers, and the government can gain more valuable information about people who may be at risk for negative psychological outcomes during the pandemic or who are not implementing protective behavior. The tool can be used in hospitals to quickly screen the level of fear in patients and minimize its severe adverse consequences.
Pilch et al. (2021) Experiencing fear during the pandemic: validation of the fear of COVID-19 scale in Polish. PeerJ 9:e11263 https://doi.org/10.7717/peerj.11263
NFIB promotes the migration and progression of kidney renal clear cell carcinoma by regulating PINK1 transcription
Kidney renal clear cell carcinoma (KIRC) is the most common and aggressive type of renal cell carcinoma. Due to high mortality rate, high metastasis rate and chemical resistance, the prognosis of KIRC patients is poor. Therefore, it is necessary to study the mechanisms of KIRC development and to develop more effective prognostic molecular biomarkers to help clinical patients. In our study, we used The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases to investigate that the expression of nuclear factor I B (NFIB) is significantly higher in KIRC than in adjacent tissues. Moreover, NFIB expression levels are associated with multiple clinical pathological parameters of KIRC, and KIRC patients with high NFIB expression have poor prognosis, suggesting that NFIB may play vital roles in the malignant development of KIRC. Further studies demonstrated that NFIB could promote the progression and metastasis of KIRC and participate in the regulation of PTEN induced kinase 1 (PINK1). Furthermore, we used chromatin immunoprecipitation (ChIP) experiments to confirm that NFIB binds to the PINK1 promoter and regulates its expression at the transcriptional level. Further experiments also confirmed the important roles of PINK1 in promoting the development of tumors by NFIB. Hence, our data provide a new NFIB-mediated regulatory mechanism for the tumor progression of KIRC and suggest that NFIB can be applied as a new predictor and therapeutic target for KIRC.
Wang et al. (2021) NFIB promotes the migration and progression of kidney renal clear cell carcinoma by regulating PINK1 transcription. PeerJ 9:e10848 https://doi.org/10.7717/peerj.10848
Soil fertility evaluation and spatial distribution of grasslands in Qilian Mountains Nature Reserve of eastern Qinghai-Tibetan Plateau
The study assessed the overall soil characteristics of grasslands on Qilian Mountains and rated the soil nutrient status with classification standard of the second national soil survey of China. Nemerow index method was used to evaluate the soil fertility of different grassland types. GIS was used to analyze the spatial distribution of the soil nutrients and provided a database for the grassland’s ecological protection and restoration. The study graded the soil organic matter (SOM), total N, and available K at level 2 (high) or above for most regions, available soil-P at level 4, while the soil bulk density, total porosity and pH were 0.77–1.32 g cm−3, 35.36–58.83% and 7.63–8.54, respectively. The rank of comprehensive soil fertility index was temperate steppe (TS) > alpine meadow (AM) > alpine steppe (AS) >upland meadow (UM) >alpine desert (AD)> lowland meadow (LM)> temperate desert steppe (TDS)> temperate desert (TD). The areas with high, medium and low soil fertility accounted for 63.19%, 34.24% and 2.57% of the total grassland area. Soil fertility of different grassland types had different main limiting factors, for instance, the pH, total N and SOM were the main factors limiting soil fertility in LM, while pH and available P were the main factors limiting soil fertility in UM, AM, TS and AS. In summary, the grassland soil fertility was generally at the mid-upper level, and the main limiting factors were found in the different types of the grasslands and their spatial distributions were figured out. Our findings also indicated that the typical grasslands and meadows may require phosphorus application, while for desert grasslands, both nitrogen and phosphorus were required to improve their comprehensive soil fertility and grassland productivity.
Li et al. (2021) Soil fertility evaluation and spatial distribution of grasslands in Qilian Mountains Nature Reserve of eastern Qinghai-Tibetan Plateau. PeerJ 9:e10986 https://doi.org/10.7717/peerj.10986
Porphyromonas gingivalis lipopolysaccharide promotes T-hel per17 cell differentiation by upregulating Delta-like ligand 4 expression on CD14+ monocytes
Backgroud To investigate the effect and mechanism of Porphyromonas gingivalis (P. gingivalis) lipopolysaccharide (LPS) on Th17 cell differentiation mediated by CD14+ monocytes. Methods P. gingivalis LPS-activated CD14+ monocytes were co-cultured with CD4+T cells in different cell ratios. An indirect co-culture system was also established using transwell chambers. Furthermore, anti- Delta-like ligand 4 (Dll-4) antibody was used to investigate the role of Dll-4 in Th17 cell response. The mRNA expression was analyzed using quantitative reverse transcription-polymerase chain reaction, and secreted cytokines in culture supernatant were detected using enzyme-linked immunosorbent assay. Flow cytometry was used to determine the frequencies of Th17 cells. IL-17 protein expression levels were determined using western blotting assay. Results P. gingivalis LPS increased the expressions of interleukin (IL)-1β, IL-6, IL-23 and transforming growth factor (TGF)-β in CD14+ monocytes. Th17 cell frequency upregulated, which is not solely cytokine-dependent but rather requires cell-cell contact with activated monocytes, particularly in the 1:10 cell ratio. Furthermore, P. gingivalis LPS increased t he expression of Dll-4 on CD14+ monocytes, whereas the anti- Dll-4 a ntibody decreased the response of Th17 cells. The results suggest that P. gingivalis LPS enhances Th17 cell response via Dll-4 upregulation on CD14+ monocytes.
Zhang et al. (2021) Porphyromonas gingivalis lipopolysaccharide promotes T-hel per17 cell differentiation by upregulating Delta-like ligand 4 expression on CD14+ monocytes. PeerJ 9:e11094 https://doi.org/10.7717/peerj.11094
Re-positive of SARS-CoV-2 test is common in COVID-19 patients after hospital discharge. Data from high standard post-discharge quarantined patients in Macao SAR, China
During the pandemic of COVID-19, Macau faces tremendous pressure because it is a famous gambling and tourism city with the world’s highest population density. The Macau government implemented decisive public health intervention to control the transmission of COVID-19, and there were only two independent outbreaks in Macau. In the second outbreak, all 35 cases were infected in foreign countries. They were quarantined in airborne infection isolation rooms for at least 14 days with reverse transcription-polymerase chain reaction (RT-PCR) tests after hospital discharge. Twelve (34.3%) of them had re-positive SARS-CoV-2 test results, and none of them presented any COVID-19 signs or symptoms during the entire quarantine period. In this study, the re-positive patients were more likely to be diagnosed in the early stage of the disease with a longer hospital stay. Virus re-infection is impossible in this high standard isolation setting, and reactivation is also unlikely, so that residual virus nucleic acid should be the possible reason for this phenomenon. Due to limited data about the risk of re-positive patients, it is better to quarantine patients after discharge for a prolonged period with repeat RT-PCR tests to minimize the community’s potential risk, particularly in the regions with relative plenty of resources and low community infection rate such as Macau.
Wong et al. (2021) Re-positive of SARS-CoV-2 test is common in COVID-19 patients after hospital discharge. Data from high standard post-discharge quarantined patients in Macao SAR, China. PeerJ 9:e11170 https://doi.org/10.7717/peerj.11170