Evaluation of SARS-CoV-2 RNA quantification by RT-LAMP compared to RT-qPCR

INTRODUCTION

Coronavirus disease 2019 (COVID-19) is a global pandemic caused by a novel virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral load of SARS-CoV-2 is associated with mortality in COVID-19 patients. Measurement of viral load requires the use of reverse transcription quantitative PCR (RT-qPCR), which in turn requires advanced equipment and techniques. In this study, we aimed to evaluate the viral load measurement using reverse transcription loop-mediated isothermal amplification (RT-LAMP), which is a simpler procedure compared to RT-qPCR.

MATERIALS AND METHODS

RNA was extracted by using the QIAamp Viral RNA Mini Kit. The RT-LAMP assay was performed by using the Loopamp® 2019-SARS-CoV-2 detection reagent kit and 10-fold serial dilutions of known viral load RT-LAMP were used to measure Tt, which is the time until the turbidity exceeds the threshold. Based on the relationship between viral load and Tt, the linearity and detection sensitivity of the calibration curve were evaluated. In addition, 117 clinical specimens were measured, and RT-qPCR and RT-LAMP assay results were compared.

RESULTS

The dilution linearity of the calibration curve was maintained at five orders of magnitude 1.0× 10⁶ to 1.0 × 10¹ copies/μL, and was confirmed to be detectable down to 1.0 × 10⁰ copies/μL. The limit of quantification of RNA extracted from clinical specimens using RT-LAMP correlated well with that obtained using RT-qPCR (r² = 0.930).

CONCLUSION

The findings indicate that RT-LAMP is an effective method to determine the viral load of SARS-CoV-2.

Antemortem inhibition of phosphoinositide 3-kinase causes changes in meat quality traits in broiler chickens

Phosphoinositide 3-kinase (PI3K) is an enzyme that mediates endocrinological responses, such as intracellular signaling of insulin and growth factors, and plays important roles in muscle homeostasis and growth. In this study, the effect of antemortem PI3K activity on meat quality traits was investigated using broiler chickens whose PI3K was inhibited pharmacologically. Breast and thigh muscles were harvested from broilers treated with the PI3K inhibitor wortmannin, and meat quality traits were evaluated by determination of color, water-holding capacity, and breaking strength. The pH and concentrations of glycogen and free amino acids were also investigated as determinants of the chemical properties of meat. The results indicated that antemortem PI3K inhibition by wortmannin modified breast muscle color with lower L∗ values (P < 0.05) and b∗ values (P < 0.05) and higher a∗ values (P < 0.05). Antemortem PI3K inhibition also increased the water-holding capacity of breast muscles (P < 0.05), although breaking strength was not much affected. In addition, antemortem PI3K inhibition increased the concentrations of free amino acids in breast muscles, especially arginine (P < 0.05) and glutamic acid (P < 0.05). Similar effects were observed in thigh muscles. Lower glycogen levels at sacrifice (P < 0.05) and the resultant higher pH during the postmortem period (P < 0.05) were associated with PI3K inhibition-induced changes in meat quality traits. The wortmannin-treated muscles shared certain features with dark, firm, and dry meat which is a common abnormal meat. These findings suggest that antemortem PI3K activity contributes to meat quality traits and is involved in the molecular mechanism of the production of meat quality abnormalities.

A catalog of associations between rare coding variants and COVID-19 outcomes

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable at https://rgc-covid19.regeneron.com.

[The inhibitors of the apical sodium-dependent bile acid transporter (ASBT) as promising drugs]

Inhibition of the apical sodium-dependent bile acid transporter (ASBT, also known as IBAT - ileal bile acid transporter, SLC10A2) leads to disruption of the enterohepatic circulation of bile acids and their excretion with fecal masses. This is accompanied by cholesterol utilization for synthesis of new bile acids. ASBT inhibitors are promising drugs for the treatment of such diseases as non-alcoholic fatty liver disease, non-alcoholic steatohepatitis, type 2 diabetes mellitus, necrotic enterocolitis, chronic constipation, atherosclerosis. To date the most known chemically synthesized inhibitors are: A3309, SHP626, A4250, 264W94, GSK2330672, SC-435. All of them are at different stages of clinical trials, which confirm the high efficacy and good tolerance of these inhibitors. Current trends in this field also include directed chemical synthesis of ASBT inhibitors, as well as their search among substances of plant origin.

TEMPORAL CHANGES IN RADIOCESIUM DEPOSITION ON THE FUKUSHIMA FLOODPLAIN

There has been significant concern about increases in the exposure dose in living areas due to the accumulation of radiocesium discharged from contaminated mountainous forests in Fukushima. In this study, we investigated the history of radiocesium deposition on several floodplains in Fukushima following the nuclear power plant accident. Radiocesium concentrations in river suspended particles and the air dose rates on the floodplains were observed continuously. The annual sediment accumulation on the floodplains was 5.5-200 kg m-2, and the observed radiocesium concentration decreased with the decrease in the radiocesium concentration of suspended particles. The air dose rates on the floodplains were gradually decreasing with time. In 2015, with heavy flood discharge, a sediment accumulation of 180-200 kg m-2 and a sharp decrease in the air dose rate were observed at the Takase River, which does not have a reservoir. Conversely, the sediment accumulation at the Ukedo River was significantly reduced due to deposition in an upstream reservoir.

Periocular injection of candesartan-PLGA microparticles inhibits laser-induced experimental choroidal neovascularization

Purpose

Microparticle technology enables local administration of medication. The purpose of this study was to examine the inhibitory effect of locally administered candesartan (CAN)-encapsulated microparticles on experimental choroidal neovascularization (CNV).

Methods

Laser photocoagulation was used to induce CNV in Brown Norway rats. The rats were pretreated with subconjunctival injections of CAN (5.0 mg/eye) or phosphate buffer saline for 3 days before photocoagulation. The volume of CNV was evaluated 7 days after laser injury using the lectin staining technique. The infiltration of macrophages within the CNV lesion was determined using immunofluorescent staining with an anti-CD68 antibody. mRNA levels of MCP-1, IL1-β and VEGF in the retinal pigment epithelium/choroid complex were determined using quantitative PCR (q-PCR).

Results

CNV volume was significantly suppressed by the treatment with CAN compared with that in vehicle-treated eyes (P<0.05, two-tailed Student’s t-test). Subconjunctival injections of CAN decreased the numbers of CD68⁺ cells in the CNV lesion. The increased mRNA levels of MCP-1, IL1-β, and VEGF induced by photocoagulation was significantly suppressed following the local administration of CAN (P<0.05, two-tailed Student’s t-test).

Conclusion

Local administration of CAN inhibited experimentally induced CNV possibly through anti-inflammatory effects.

The effect of regioisomerism on the photophysical properties of alkylated-naphthalene liquids

Novel alkylated naphthalene liquids with a correlation among the 1- and 2-regioisomeric chemical structures and their photophysical, calorimetric and rheological properties are presented.

Multi-imaging of Cytokinin and Abscisic Acid on the Roots of Rice (Oryza sativa) Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Plant hormones act as important signaling molecules that regulate responses to abiotic stress as well as plant growth and development. Because their concentrations of hormones control the physiological responses in the target tissue, it is important to know the distributions and concentrations in the tissues. However, it is difficult to determine the hormone concentration on the plant tissue as a result of the limitations of conventional methods. Here, we report the first multi-imaging of two plant hormones, one of cytokinin [i.e., trans-zeatin (tZ)] and abscisic acid (ABA) using a new technology, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) imaging. Protonated signals of tZ (m/z 220.1) and ABA (m/z 265.3) were chosen on longitudinal sections of rice roots for MS imaging. tZ was broadly distributed about 40 mm behind the root apex but was barely detectable at the apex, whereas ABA was mainly detected at the root apex. Multi-imaging using MALDI-TOF-MS enabled the visualization of the localization and quantification of plant hormones. Thus, this tool is applicable to a wide range of plant species growing under various environmental conditions.

Susceptibility of isogeneic ginbuna Carassius auratus langsdorfii Temminck et Schlegel to cyprinid herpesvirus-2 (CyHV-2) as a model species

Herpesviral haematopoietic necrosis (HVHN), caused by cyprinid herpesvirus-2 (CyHV-2), has affected the commercial production of the goldfish Carassius auratus and gibelio carp Carassius auratus gibelio. High water temperature treatments are reported to reduce the mortality rate of infected goldfish and elicit immunity in the survivors. To define the mechanism by which this intervention induces resistance, clonal ginbuna Carassius auratus langsdorfii, which is closely related to both species and has been used in fish immunology, may represent a promising model species. In this study, we investigated the susceptibility of clonal ginbuna strains to CyHV-2 and the effect of high water temperature treatment on infected ginbuna and goldfish. Experimental intraperitoneal infection with CyHV-2 at 25 °C caused 100% mortality in ginbuna strains, which was accompanied by histopathological changes typical of HVHN. Both infected ginbuna S3n strain and goldfish, exposed to high temperature for 6 days [shifting from 25 °C (permissive) to 34 °C (non-permissive)], showed reduced mortalities after the 1st inoculation, and subsequent 2nd virus challenge to 0%, indicating induction of immunity. It was concluded that ginbuna showed a similar susceptibility and disease development in CyHV-2 infection compared to goldfish, suggesting that ginbuna can be a useful fish model for the study of CyHV-2 infection and immunity.

Caries-related Bacteria and Cytokines Induce CXCL10 in Dental Pulp

Marked infiltration of inflammatory cells, such as activated T-cells, is observed in the progression of pulpitis; however, little is known about the mechanism of their recruitment into pulpal lesions. It has been recently demonstrated that CXC chemokine ligand 10 (CXCL10) chemoattracts CXC chemokine receptor 3 (CXCR3)-positive activated T-cells. We therefore examined whether CXCL10 is involved in the pathogenesis of pulpitis. CXCL10 mRNA expression levels in clinically inflamed dental pulp were higher than those in healthy dental pulp. Immunostaining results revealed that CXCL10 was detected in macrophages, endothelial cells, and fibroblasts in inflamed dental pulp, and that CXCR3 expression was observed mainly on T-cells. Moreover, cultured dental pulp fibroblasts produced CXCL10 after stimulation with live caries-related bacteria, peptidoglycans, and pro-inflammatory cytokines. In contrast, heat-killed bacteria did not induce CXCL10 secretion. These findings suggest that CXCL10-CXCR3 may play an important role in the pulpal immune response to caries-related bacterial invasion. Abbreviations: CXCL10, CXC chemokine ligand 10; CXCR3, CXC chemokine receptor 3; IFN, interferon; FBS, fetal bovine serum; LTA, lipoteichoic acid; PGN, peptidoglycan; IL, interleukin; TNF, tumor necrosis factor; PBS, phosphate-buffered saline; ELISA, enzyme-linked immunosorbent assay; CCL, C-C chemokine ligand; TLR, Toll-like receptor; NOD, nucleotide oligomerization domain; HDPF, human dental pulp fibroblasts.

New approaches towards laboratory diagnosis of isolated sulphite oxidase deficiency

Background: Molybdenum cofactor deficiency (resulting in combined deficiencies of the enzymes sulphite oxidase, xanthine dehydrogenase and aldehyde dehydrogenase) and isolated sulphite oxidase deficiency are inherited metabolic diseases which follow an autosomal recessive trait of inheritance. Detection of these diseases in selective screening for inborn errors of metabolism is not easy because relevant metabolites are either not routinely determined or are unstable.

Methods: We have searched for additional markers for these diseases and studied plasma total homocysteine (determined by enzyme immunoassay) and S-sulphonation of transthyretin (assessed by electrospray ionization mass spectrometry).

Results and conclusion: We found total homocysteine concentrations below the limit of quantification (<1 µmol/L) in all samples of patients with sulphite oxidase deficiency studied in this regard and that the proportion of S-sulphonated transthyretin is clearly increased in such samples. Our observations suggest additional tools for selective screening and diagnostic work-up of patients suspected of having sulphite oxidase deficiency.

[Upcoming Challenges of Next-Generation Clinical Laboratory Tests with Mass Spectrometric Technique -Chairman's Introductory Remarks -]

Many medical researchers and technologists have measured proteins, hormones, lipids, carbohydrates, and nucleotides in body fluids using conventional analytical techniques. After the 1990s, -omics devices includ- ing soft ionization mass spectrometry produced by Prof. John B Fenn and Dr. Koichi Tanaka en'abled us to more easily detect and identify new bioactive molecules in body fluids for the rapid and differential diagnosis of diseases. Especially, the MS techniques are leading to new breakthroughs in the fields of microorganism identification and pathological diagnosis. In this symposium, upcoming challenges of the modern MS techniques, such as electrospray ionization- and matrix-assisted laser desorption ionization-MS, in clinical tests for discovering biomarkers are being presented for the rapid diagnoses of infectious diseases and amyloidosis, and rapid detections of hormones and lipids in clinical samples by 4 speakers. [Review].

Fluorescent liquid pyrene derivative-in-water microemulsions

Using a liquid pyrene derivative as the oil, stable oil-in-water microemuslions are prepared, with tunable fluorescence emission via droplet size.

Visible luminescent lanthanide ions and a large π-conjugated ligand system shake hands

The novel photophysics induced by the combination of visible luminescent europium(iii) ions and large π-conjugated systems are described.

[Rapid Identification of Infectious Microorganisms in Clinical Samples by MALDI-TOF MS Analysis]

Matrix-laser desorption ionization time-of flight/mass spectrometry (MALDI-TOF MS) is a powerful tool for the detection of target molecules in body fluids. Recently, the MALDI-TOF MS technique was applied for the rapid detection of protein profiles in cultured strains, and has rapid, simple, and universal advantages over the conventional technique. MALDI mass patterns were compared with the unique ribosomal 16S protein profiles of standard microorganism strains in a commercial database. Although this present MS technique has already been adopted as a routine method for the identification of general bacteria in the clinical laboratory field, there are still many problems to overcome regarding current challenges, necessitating the identification of more valuable species of microorganism. As the first step, we have begun the standardization of sample preparation to identify species causing infectious diseases by MALDI-TOF MS. In this special issue, we summarize the challenges in the modified preparation of clinical samples, such as blood, urine, and sputum, in our laboratory to rapidly diagnose severe infectious disease, and describe the current trends in clinical microbiology.

Luminescent lanthanide coordination polymers for photonic applications

Luminescent lanthanide coordination polymers composed of lanthanide ions and organic joint ligands exhibit characteristic photophysical and thermostable properties that are different from typical organic dyes, luminescent metal complexes, and semiconductor nanoparticles.

Stress-induced ceramide generation and apoptosis via the phosphorylation and activation of nSMase1 by JNK signaling

Neutral sphingomyelinase (nSMase) activation in response to environmental stress or inflammatory cytokine stimuli generates the second messenger ceramide, which mediates the stress-induced apoptosis. However, the signaling pathways and activation mechanism underlying this process have yet to be elucidated. Here we show that the phosphorylation of nSMase1 (sphingomyelin phosphodiesterase 2, SMPD2) by c-Jun N-terminal kinase (JNK) signaling stimulates ceramide generation and apoptosis and provide evidence for a signaling mechanism that integrates stress- and cytokine-activated apoptosis in vertebrate cells. An nSMase1 was identified as a JNK substrate, and the phosphorylation site responsible for its effects on stress and cytokine induction was Ser-270. In zebrafish cells, the substitution of Ser-270 for alanine blocked the phosphorylation and activation of nSMase1, whereas the substitution of Ser-270 for negatively charged glutamic acid mimicked the effect of phosphorylation. The JNK inhibitor SP600125 blocked the phosphorylation and activation of nSMase1, which in turn blocked ceramide signaling and apoptosis. A variety of stress conditions, including heat shock, UV exposure, hydrogen peroxide treatment, and anti-Fas antibody stimulation, led to the phosphorylation of nSMase1, activated nSMase1, and induced ceramide generation and apoptosis in zebrafish embryonic ZE and human Jurkat T cells. In addition, the depletion of MAPK8/9 or SMPD2 by RNAi knockdown decreased ceramide generation and stress- and cytokine-induced apoptosis in Jurkat cells. Therefore the phosphorylation of nSMase1 is a pivotal step in JNK signaling, which leads to ceramide generation and apoptosis under stress conditions and in response to cytokine stimulation. nSMase1 has a common central role in ceramide signaling during the stress and cytokine responses and apoptosis.

Catechins inhibit vascular endothelial growth factor production and cyclooxygenase-2 expression in human dental pulp cells

AIM

To investigate the effect of catechins on vascular endothelial growth factor (VEGF) production and cyclooxygenase-2 (COX-2) expression in human dental pulp cells (HDPC) stimulated with bacteria-derived factors or pro-inflammatory cytokines.

METHODOLOGY

Morphologically fibroblastic cells established from explant cultures of healthy human dental pulp tissues were used as HDPC. HDPC pre-treated with catechins, epigallocatechin-3-gallate (EGCG) or epicatechin gallate (ECG), were exposed to lipopolysaccharide (LPS), peptidoglycan (PG), interlukin-1β (IL-1β) or tumour necrosis factor-α (TNF-α). VEGF production was examined by enzyme-linked immunosorbent assay, and COX-2 expression was assessed by immunoblot.

RESULTS

EGCG and ECG significantly reduced LPS- or PG-mediated VEGF production in the HDPC in a dose-dependent manner. EGCG also prevented IL-1β-mediated VEGF production. Although TNF-α did not enhance VEGF production in the dental pulp cells, treatment of 20 μg mL(-1) of EGCG decreased the level of VEGF. In addition, the catechins attenuated COX-2 expression induced by LPS and IL-1β.

CONCLUSIONS

The up-regulated VEGF and COX-2 expressions in the HDPC stimulated with these bacteria-derived factors or IL-1β were diminished by the treatment of EGCG and ECG. These findings suggest that the catechins may be beneficial as an anti-inflammatory tool of the treatment for pulpal inflammation.