Rapid and visual detection of 2019 novel coronavirus (SARS-CoV-2) by a reverse transcription loop-mediated isothermal amplification assay

OBJECTIVE

To evaluate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and compare it with RT-PCR.

METHODS

We designed primers specific to the orf1ab and S genes of SARS-CoV-2. Total viral RNA was extracted using the QIAamp Viral RNA Mini Kit. We optimized the RT-LAMP assay, and evaluated it for its sensitivity and specificity of detection using real-time turbidity monitoring and visual observation.

RESULTS

The primer sets orf1ab-4 and S-123 amplified the genes in the shortest times, the mean (±SD) times were 18 ± 1.32 min and 20 ± 1.80 min, respectively, and 63°C was the optimum reaction temperature. The sensitivities were 2 × 10¹ copies and 2 × 10² copies per reaction with primer sets orf1ab-4 and S-123, respectively. This assay showed no cross-reactivity with 60 other respiratory pathogens. To describe the availability of this method in clinical diagnosis, we collected 130 specimens from patients with clinically suspected SARS-CoV-2 infection. Among them, 58 were confirmed to be positive and 72 were negative by RT-LAMP. The sensitivity was 100% (95% CI 92.3%-100%), specificity 100% (95% CI 93.7%-100%). This assay detected SARS-CoV-2 in a mean (±SD) time of 26.28 ± 4.48 min and the results can be identified with visual observation.

CONCLUSION

These results demonstrate that we developed a rapid, simple, specific and sensitive RT-LAMP assay for SARS-CoV-2 detection among clinical samples. It will be a powerful tool for SARS-CoV-2 identification, and for monitoring suspected patients, close contacts and high-risk groups.

A Conducting Polymer Film Stronger Than Aluminum

Polythiophene (Pth) was electrochemically deposited onto stainless steel substrate from freshly distilled boron fluoride-ethyl ether containing 10 millimoles of thiophene per liter. The free-standing Pth film obtained at an applied potential of 1.3 volts (versus Ag/AgCl) had a conductivity of 48.7 siemens per centimeter. Its tensile strength (1200 to 1300 kilograms per square centimeter) was greater than that of aluminium (1000 to 1100 kilograms per square centimeter). This Pth film behaves like a metal sheet and can be easily cut into various structures with a knife or a pair of scissors.

Rubbing-induced molecular reorientation on an alignment surface of an aromatic polyimide containing cyanobiphenyl side chains

Surface lamellar decoration (SLD), surface enhanced Raman scattering (SERS) and optical second harmonic generation (SHG) experiments have been utilized to study the molecular orientation and conformation changes at a rubbed polyimide alignment-layer surface. This aromatic polyimide containing pendent cyanobiphenyl mesogens was synthesized via a polycondensation of 2,2'-bis(3,4-dicarboxy-phenyl)hexafluoropropane dianhydride (6FDA) with bis[omega-[4-(4-cyanophenyl)phenoxy]hexyl] 4,4'-diamino-2,2'-biphenyldicarboxylate (nCBBP, n = 6), abbreviated as 6FDA--6CBBP. Uniform alignment layers, possessing high pretilt angles ranging from 39 degrees to 43 degrees, have been achieved after mechanical rubbing of the polyimide thin film surface at room temperature and subsequent annealing. This is the first time that high pretilt angles have been detected to possess a negative angle (-theta(c)) with respect to the rubbing direction (i.e., opposite to the rubbing direction), considerably different from the conventional pretilt angle (theta(c)) observed along the rubbing direction. This observation is confirmed using magnetic null and SHG methods. Combined polyethylene (PE) SLD and atomic force microscopy experiments reveal that the azimuthal orientation distribution of the long axis of the edge-on PE lamellar crystals is oriented normal to the rubbing direction, indicating that the PE chains are aligned parallel to the rubbing direction. This SLD technique probes the anisotropic surface orientation of the outermost molecules of the rubbed polyimide layer. The SERS results show that prior to rubbing the surface, both the pendent cyanobiphenyls in the side chains and backbones possess nearly planar chain conformations at the polyimide surface. Mechanical rubbing causes not only tilting of the backbone moieties, such as imide-phenylene structure, but also significant conformational rearrangements of the pendent side chains at the surfaces. The molecular mechanism of this unusual alignment is due to the fact that the pendent cyanobiphenyls forms a uniformly tilted conformation on the rubbed surface, and the polar cyano groups point down toward the layer surface deduced from SHG phase measurements. This conformational rearrangement of the side chains results in the formation of fold-like bent structures on the surface, which directly leads to the long axis of cyanobiphenyls having the -theta(c) pretilt angle with respect to the rubbing direction.

c-Myc-mediated repression of miR-15-16 in hypoxia is induced by increased HIF-2α and promotes tumor angiogenesis and metastasis by upregulating FGF2

Previous studies have established the link between aberrant microRNA (miRNA) expression and hypoxia in various neoplasms. However, how these hypoxia-related miRNAs modulate tumor progression is still unclear. Therefore, the patterns of miRNA in colorectal carcinoma cell lines in response to hypoxia or not were first screened and the hypoxia-induced repression of the miR-15-16 cluster was confirmed. Then, this repression was found to be associated with high tumor stage and poor prognosis in colorectal carcinoma and is shown to promote tumor angiogenesis and metastasis by the loss of restriction of its target gene, fibroblast growth factor-2 (FGF2). Moreover, the general and alterative promoters of the miR-15-16 host (deleted in lymphocytic leukemia 2, DLEU2) were mapped, and three c-Myc/Max binding sites in response to the hypoxia-induced repression of miR-15-16 were further identified. Finally, an enhanced stability of c-Myc/Max heterodimer promoted by increased hypoxia-inducible factor-2α (HIF-2α) was validated, and we also verified that the enhancement contributed to the hypoxia-induced repression of miR-15-16. In brief, the c-Myc-mediated transcriptional repression of miR-15-16 in hypoxia is induced by increased HIF-2α and promoted tumor angiogenesis and hematogenous metastasis by the further loss of post-transcriptional inhibition of FGF2. Our study provides a better understanding of the coping mechanisms in response to tumor hypoxia and may be helpful in developing an effective prognostic marker or treatment target against solid tumors.

COMT rs4680 Met is not always the 'smart allele': Val allele is associated with better working memory and larger hippocampal volume in healthy Chinese

Catechol-O-methyltransferase (COMT) Val158Met (rs4680) polymorphism plays a crucial role in regulating brain dopamine level. Converging evidence from Caucasian samples showed that, compared with rs4680 Val allele, the Met allele was linked to lower COMT activity, which in turn was linked to better cognitive performance such as working memory (WM) and to a larger hippocampus (a brain region important for WM). However, some behavioral studies have shown that the function of rs4680 appears to vary across different ethnic groups, with Chinese subjects showing an opposite pattern as that for Caucasians (i.e. the Val allele is linked to better cognitive functions related to WM in Chinese). Using a sample of healthy Han Chinese college students (ages from 19 to 21 years), this study investigated the association of COMT Val158Met genotype with behavioral data on a two-back WM task (n = 443, 189M/254F) and T1 MRI data (n = 320, 134M/186F). Results showed that, compared to the Met allele, the Val allele was associated with larger hippocampal volume (the right hippocampus: β = -0.118, t = -2.367, P = 0.019, and the left hippocampus: β = -0.099, t = -1.949, P = 0.052) and better WM performance (β = -0.110, t = -2.315, P = 0.021). These results add to the growing literature on differentiated effects of COMT rs4680 polymorphism on WM across populations and offer a brain structural mechanism for such population-specific genetic effects.

Carcinoma of the minor salivary glands: results of surgery and combined therapy

PURPOSE

This article reports the results of treatment of 7 histologic types of minor salivary gland carcinoma.

PATIENTS AND METHODS

Of 256 cases, local excision was used in 194, extended excision in 62, excision accompanied by neck dissection in 98, and surgery with adjunctive radiation therapy or chemotherapy in 101. Forty-five of the 98 neck dissection cases had cervical node metastases.

RESULTS

Survival rates were analyzed for 233 patients. The 3-year survival rate was (167 of 215) (77.67%), the 5-year survival rate was 134 of 187 (71.76%), and the 10-year survival rate was 79 of 113 (69.91%).

CONCLUSIONS

These data confirm that surgery is still the mode of choice in the treatment of minor salivary gland carcinoma, but a combination with radiation therapy or chemotherapy is advisable in some patients.

Multiplexed capillary zone electrophoresis and micellar electrokinetic chromatography with internal standardization

Although liquid chromatography and gas chromatography are the main workhorses in the analytical laboratory, samples can only be analyzed consecutively in an instrument. In this study, capillary zone electrophoresis and micellar electrokinetic chromatography separations are performed in a 96-capillary array system with laser-induced fluorescence detection. Migration times of four kinds of fluoresceins and six polyaromatic hydrocarbons (PAHs) are normalized to one of the capillaries using two internal standards. The relative standard deviations after normalization are 0.6-1.4% for the fluoresceins and 0.1-1.5% for the PAHs. Quantitative calibration of the separations based on peak areas is also performed, again with substantial improvement over the raw data. This opens up the possibility of performing massively parallel separations for high-throughput chemical analysis for process monitoring, combinatorial synthesis, and clinical diagnosis.

Selective detection of individual DNA molecules by capillary polymerase chain reaction

On-line capillary polymerase chain reaction (PCR) coupled with laser-induced fluorescence detection was successfully demonstrated for individual DNA molecules. A single 30-microm-i.d. fused-silica capillary was used both as the reaction vessel and for isolating single molecules. SYBR green I dye was added into the reaction mixture for dynamic fluorescent labeling. Because of the small inside diameter of the capillary, PCR-amplified DNA fragments from single molecules were localized in the capillary, providing discrete product zones with concentrations at readily detectable levels. By counting the number of peaks in the capillary via electromigration past a detection window, the number of starting DNA molecules could be determined. With selective primer design, only the molecule of interest was detected. Amplification of the 110-bp fragment from an individual human beta-globin gene and the 142-bp fragment from an individual HIV-1 DNA was demonstrated. This opens the possibility of highly selective and sensitive disease diagnosis at a very early stage.

Assessment of biodiversity in Chilean cattle using the distribution of major histocompatibility complex class II BoLA-DRB3 allele

Bovine leukocyte antigens (BoLAs) are used extensively as markers for bovine disease and immunological traits. In this study, we estimated BoLA-DRB3 allele frequencies using 888 cattle from 10 groups, including seven cattle breeds and three crossbreeds: 99 Red Angus, 100 Black Angus, 81 Chilean Wagyu, 49 Hereford, 95 Hereford × Angus, 71 Hereford × Jersey, 20 Hereford × Overo Colorado, 113 Holstein, 136 Overo Colorado, and 124 Overo Negro cattle. Forty-six BoLA-DRB3 alleles were identified, and each group had between 12 and 29 different BoLA-DRB3 alleles. Overo Negro had the highest number of alleles (29); this breed is considered in Chile to be an 'Old type' European Holstein Friesian descendant. By contrast, we detected 21 alleles in Holstein cattle, which are considered to be a 'Present type' Holstein Friesian cattle. Chilean cattle groups and four Japanese breeds were compared by neighbor-joining trees and a principal component analysis (PCA). The phylogenetic tree showed that Red Angus and Black Angus cattle were in the same clade, crossbreeds were closely related to their parent breeds, and Holstein cattle from Chile were closely related to Holstein cattle in Japan. Overall, the tree provided a thorough description of breed history. It also showed that the Overo Negro breed was closely related to the Holstein breed, consistent with historical data indicating that Overo Negro is an 'Old type' Holstein Friesian cattle. This allelic information will be important for investigating the relationship between major histocompatibility complex (MHC) and disease.

Effect of clonal integration on nitrogen cycling in rhizosphere of rhizomatous clonal plant, Phyllostachys bissetii, under heterogeneous light

Clonal integration plays an important role in clonal plant adapting to heterogeneous habitats. It was postulated that clonal integration could exhibit positive effects on nitrogen cycling in the rhizosphere of clonal plant subjected to heterogeneous light conditions. An in-situ experiment was conducted using clonal fragments of Phyllostachys bissetii with two successive ramets. Shading treatments were applied to offspring or mother ramets, respectively, whereas counterparts were treated to full sunlight. Rhizomes between two successive ramets were either severed or connected. Extracellular enzyme activities and nitrogen turnover were measured, as well as soil properties. Abundance of functional genes (archaeal or bacterial amoA, nifH) in the rhizosphere of shaded, offspring or mother ramets were determined using quantitative polymerase chain reaction. Carbon or nitrogen availabilities were significantly influenced by clonal integration in the rhizosphere of shaded ramets. Clonal integration significantly increased extracellular enzyme activities and abundance of functional genes in the rhizosphere of shaded ramets. When rhizomes were connected, higher nitrogen turnover (nitrogen mineralization or nitrification rates) was exhibited in the rhizosphere of shaded offspring ramets. However, nitrogen turnover was significantly decreased by clonal integration in the rhizosphere of shaded mother ramets. Path analysis indicated that nitrogen turnover in the rhizosphere of shaded, offspring or mother ramets were primarily driven by the response of soil microorganisms to dissolved organic carbon or nitrogen. This unique in-situ experiment provided insights into the mechanism of nutrient recycling mediated by clonal integration. It was suggested that effects of clonal integration on the rhizosphere microbial processes were dependent on direction of photosynthates transport in clonal plant subjected to heterogeneous light conditions.

Germline hMSH2 promoter mutation in a Chinese HNPCC kindred: evidence for dual role of LOH

Hereditary non-polyposis colorectal cancer (HNPCC) is a dominantly inherited cancer predisposition syndrome that is caused by germline mutations in mismatch repair genes. By screening the core promoters of hMSH2, hMLH1, and hMSH6 in 37 Chinese suspected HNPCC families, a novel germline mutation c.-78_-79delGT was found in the hMSH2 promoter. Its pathogenic effects were supported by the following findings: (a) it co-segregated with HNPCC-related cancers and was not present in the 220 control subjects, (b) tumors harboring the mutation lacked the expression of hMSH2 and showed high microsatellite instability, (c) it significantly decreased the promoter activity, and (d) it abolished the binding ability of the transcription factor E1A-F. Loss of heterozygosity (LOH) was found in three of the tumors studied. Intriguingly, in the tumors from patients II:1 and III:1, LOH occurred in the wild-type allele and agreed well with the traditional 'two-hit' model. In contrast, in the tumor from patient III:3, LOH occurred in the mutant allele. A pathogenic somatic mutation (c.2210+1G>A) was also found in this tumor; therefore, we proposed that the 'second hit' was inactivated by somatic mutation, and the mutant allele was lost during tumor progression; this provided evidence for the new hypothesis for the dual role of LOH.

Cellular and molecular modification of egg envelope hardening in fertilization

Fertilization is an essential process that fundamentally impacts fitness. An egg changes dramatically after fertilization mediating the beginning of life, which mainly includes the transformation of the egg envelope via hardening, which is thought to be due to complex reactions involved in the conversion of cellular and molecular. This review highlights the mechanisms of egg envelope hardening in teleost fish. We conclude that the egg envelope hardening might be carried out in two steps. (a) A metalloprotease (alveolin) hydrolyzes the N-terminal proline-glutamine (Pro-Gln) region of zona pellucida (ZP) 1 and (b) triggers intermolecular cross-linking to ZP3 catalyzed by transglutaminase (TGase). The post-fertilization hardening of the egg envelope is an evolutionarily conserved phenomenon across species. We discuss the biochemical function and interaction of some factors reported to be essential to egg envelope hardening in mammalian and nonmammalian species, including metalloprotease, TGase, peroxidase/ovoperoxidase, and other factors (carbohydrate moieties, zinc and Larp6 proteins), and the relevant data suggest that egg envelope hardening is crucial to block polyspermy in internal fertilization, in addition to protecting the developing embryo from mechanical shock and preventing bacterial infection in external fertilization. Increased knowledge of the processes of egg envelope hardening and fertilization is likely to make a remarkable contribution to reproduction and aquaculture.

Molecular Mechanisms of Spawning Habits for the Adaptive Radiation of Endemic East Asian Cyprinid Fishes

Despite the widespread recognition of adaptive radiation as a driver of speciation, the mechanisms by which natural selection generates new species are incompletely understood. The evolutionary radiation of endemic East Asian cyprinids has been proposed as evolving through a change in spawning habits, involving a transition from semibuoyant eggs to adhesive eggs in response to crosslinked river-lake system formation. Here, we investigated the molecular mechanisms that underpin this radiation, associated with egg hydration and adhesiveness. We demonstrated that semibuoyant eggs enhance hydration by increasing the degradation of yolk protein and accumulation of Ca2+ and Mg2+ ions, while adhesive eggs improve adhesiveness and hardness of the egg envelope by producing an adhesive layer and a unique 4th layer to the egg envelope. Based on multiomics analyses and verification tests, we showed that during the process of adaptive radiation, adhesive eggs downregulated the "vitellogenin degradation pathway," "zinc metalloprotease pathway," and "ubiquitin-proteasome pathway" and the pathways of Ca2+ and Mg2+ active transport to reduce their hydration. At the same time, adhesive eggs upregulated the crosslinks of microfilament-associated proteins and adhesive-related proteins, the hardening-related proteins of the egg envelope, and the biosynthesis of glycosaminoglycan in the ovary to generate adhesiveness. These findings illustrate the novel molecular mechanisms associated with hydration and adhesiveness of freshwater fish eggs and identify critical molecular mechanisms involved in the adaptive radiation of endemic East Asian cyprinids. We propose that these key egg attributes may function as "magic traits" in this adaptive radiation.

Effect of Intermittent and Mild Cold Stimulation on the Immune Function of Bursa in Broilers

Cold stress causes growth performance to decrease and increases production costs. Cold adaptation can enhance immune function and alleviate the negative impact caused by the stress condition. The study investigated the effect of intermittent and mild cold stimulation on the immune function of the bursa of Fabricius in broilers. A total of 400 healthy one-day-old broilers were divided into the control group (CC) and cold stimulation (CS) groups. The CC group was raised at a conventional raising temperature of broilers, while the CS groups were raised at 3°C below the temperature of the CC for three-, four-, five-, or six-hour periods at one-day intervals from 15 to 35 days of age (D35), denoted CS3, CS4, CS5, and CS6, respectively. Subsequently, they were raised at 20°C from 36 to 49 days of age (D49). The expression levels of TLRs, cytokines, and AvBDs were determined to access the immune function of bursa in broilers. After 21-day IMCS (at D36), the expression levels of TLR1, TLR15 and TLR21, interleukin (IL)-8, and interferon (IFN)-γ, as well as AvBD8 in CS groups, were lower than those in CC (p < 0.05). The expression levels of TLR3, TLR4 and TLR7, were decreased in the CS3, CS5, and CS6 groups (p < 0.05), but there were no significant differences in both the CC and CS4 groups (p > 0.05). When the IMCS ended for 14 days (at D49), the expression levels of TLR2, TLR3, TLR5, TLR7, TLR15, and TLR21, and IL-8, as well as AvBD2, AvBD4 and AvBD7 in CS groups, were lower than those in CC (p < 0.05). In addition to CS4, the expression levels of TLR1, IFN-γ, and AvBD8 in CS3, CS5, and CS6 were still lower than those in CC (p < 0.05). We concluded that the intermittent and mild cold stimulation could regulate immunoreaction by modulating the production of TLRs, cytokines, and AvBDs in the bursa, which could help broilers adapt to low ambient temperature and maintain homeostasis.

Gasification of torrefied Miscanthus × giganteus in an air-blown bubbling fluidized bed gasifier

Torrefaction is suggested to be an effective method to improve the fuel properties of biomass and gasification of torrefied biomass should provide a higher quality product gas than that from unprocessed biomass. In this study, both raw and torrefied Miscanthus × giganteus (M×G) were gasified in an air-blown bubbling fluidized bed (BFB) gasifier using olivine as the bed material. The effects of equivalence ratio (ER) (0.18-0.32) and bed temperature (660-850°C) on the gasification performance were investigated. The results obtained suggest the optimum gasification conditions for the torrefied M × G are ER 0.21 and 800°C. The product gas from these process conditions had a higher heating value (HHV) of 6.70 MJ/m(3), gas yield 2m(3)/kg biomass (H2 8.6%, CO 16.4% and CH4 4.4%) and cold gas efficiency 62.7%. The comparison between raw and torrefied M × G indicates that the torrefied M × G is more suitable BFB gasification.

On-line nanoliter cycle sequencing reaction with capillary zone electrophoresis purification for DNA sequencing

An integrated system for DNA sequencing based on a nanoreactor for cycle-sequencing reaction coupled with on-line capillary zone electrophoresis (CZE) for purification and capillary gel electrophoresis (CGE) for separation is presented. Less than 100 nl of premixed reagent solution, which includes dye-labeled terminator pre-mix, bovine serum albumin and template, was hydrodynamically injected into a fused-silica capillary (75 microm I.D.) inside a laboratory-made microthermocycler for cycle sequencing reaction. In the same capillary, the reaction products were purified by CZE followed by on-line injection of the DNA fragments into another capillary for CGE. Over 540 base pairs (bp) of DNA can be separated and the bases called for single-standed DNA with 0.9% error rate. The total time was about 3.5 h, or a cycle time of 2 h with staggered operation. For double-stranded DNA, a longer reaction time was required and base calling up to 490 bp with 1.2% error rate was achieved. The whole system is readily adaptable to automated multiplex operation for DNA sequencing or polymerase chain reaction analysis.

Role of extracellular exopolymers in biological phosphorus removal

Three sequencing batch reactors (SBRs) supplied with different carbon sources were investigated. The system supplied with glucose gained the best enhanced biological phosphorus removal (EBPR), although all of them were seeded from the same sludge. With the measurement of poly-beta-hydroxyalkanoate (PHA) concentration, phosphorus content in sludge and extracellular exopolymers (EPs) with scanning electron microscopy (SEM) combined with energy dispersive spectrometry (EDS), it was found that the biosorption effect of EPs played an important role in phosphorus removal and that the amount of PHA at the end of anaerobic phase was not the only key factor to determine the following phosphorus removal efficiency.