Real-time reverse transcription polymerase chain reaction development for rapid detection of Tomato brown rugose fruit virus and comparison with other techniques

Background: Tomato brown rugose fruit virus (ToBRFV) is a highly infectious tobamovirus that causes severe disease in tomato (Solanum lycopersicum L.) crops. In Italy, the first ToBRFV outbreak occurred in 2018 in several provinces of the Sicily region. ToBRFV outbreak represents a serious threat for tomato crops in Italy and the Mediterranean Basin. Methods: Molecular and biological characterisation of the Sicilian ToBRFV ToB-SIC01/19 isolate was performed, and a sensitive and specific Real-time RT-PCR TaqMan minor groove binder probe method was developed to detect ToBRFV in infected plants and seeds. Moreover, four different sample preparation procedures (immunocapture, total RNA extraction, direct crude extract and leaf-disk crude extract) were evaluated. Results: The Sicilian isolate ToB-SIC01/19 (6,391 nt) showed a strong sequence identity with the isolates TBRFV-P12-3H and TBRFV-P12-3G from Germany, Tom1-Jo from Jordan and TBRFV-IL from Israel. The ToB-SIC01/19 isolate was successfully transmitted by mechanical inoculations in S. lycopersicum L. and Capsicum annuum L., but no transmission occurred in S. melongena L. The developed real-time RT-PCR, based on the use of a primer set designed on conserved sequences in the open reading frames3, enabled a reliable quantitative detection. This method allowed clear discrimination of ToBRFV from other viruses belonging to the genus Tobamovirus, minimising false-negative results. Using immunocapture and total RNA extraction procedures, the real-time RT-PCR and end-point RT-PCR gave the same comparable results. Using direct crude extracts and leaf-disk crude extracts, the end-point RT-PCR was unable to provide a reliable result. This developed highly specific and sensitive real-time RT-PCR assay will be a particularly valuable tool for early ToBRFV diagnosis, optimising procedures in terms of costs and time

Detection and identification of human Plasmodium species with real-time quantitative nucleic acid sequence-based amplification

BACKGROUND: Decisions concerning malaria treatment depend on species identification causing disease. Microscopy is most frequently used, but at low parasitaemia (<20 parasites/μl) the technique becomes less sensitive and time consuming. Rapid diagnostic tests based on Plasmodium antigen detection do often not allow for species discrimination as microscopy does, but also become insensitive at <100 parasites/μl. METHODS: This paper reports the development of a sensitive and specific real-time Quantitative Nucleic Acid Sequence Based Amplification (real-time QT-NASBA) assays, based on the small-subunit 18S rRNA gene, to identify the four human Plasmodium species. RESULTS: The lower detection limit of the assay is 100 – 1000 molecules in vitro RNA for all species, which corresponds to 0.01 – 0.1 parasite per diagnostic sample (i.e. 50 μl of processed blood). The real-time QT-NASBA was further evaluated using 79 clinical samples from malaria patients: i.e. 11 Plasmodium. falciparum, 37 Plasmodium vivax, seven Plasmodium malariae, four Plasmodium ovale and 20 mixed infections. The initial diagnosis of 69 out of the 79 samples was confirmed with the developed real-time QT-NASBA. Re-analysis of seven available original slides resolved five mismatches. Three of those were initially identified as P. malariae mono-infection, but after re-reading the slides P. falciparum was found, confirming the real-time QT-NASBA result. The other two slides were of poor quality not allowing true species identification. The remaining five discordant results could not be explained by microscopy, but may be due to extreme low numbers of parasites present in the samples. In addition, 12 Plasmodium berghei isolates from mice and 20 blood samples from healthy donors did not show any reaction in the assay. CONCLUSION: Real-time QT-NASBA is a very sensitive and specific technique with a detection limit of 0.1 Plasmodium parasite per diagnostic sample (50 μl of blood) and can be used for the detection, identification and quantitative measurement of low parasitaemia of Plasmodium species, thus making it an effective tool for diagnostic purposes and useful for epidemiological and drug studies

J Occup Environ Hyg

The purpose of this article was to research and develop a direct-reading exposure assessment method that combined a real-time location system with a wireless direct-reading personal chemical sensor. The personal chemical sensor was a photoionization device for detecting volatile organic compounds. The combined system was calibrated and tested against the same four standard gas concentrations and calibrated at one standard location and tested at four locations that included the standard locations. Data were wirelessly collected from the chemical sensor every 1.4 sec, for volatile organic compounds concentration, location, temperature, humidity, and time. Regression analysis of the photo-ionization device voltage response against calibration gases showed the chemical sensor had a limit of detection of 0.2 ppm. The real-time location system was accurate to 13 cm \uc2\ub1 6 cm (standard deviation) in an open area and to 57 cm \uc2\ub1 31 cm in a closed room where the radio frequency has to penetrate drywall-finished walls. The streaming data were collected and graphically displayed as a three-dimensional hazard map for assessment of peak exposure with location. A real-time personal exposure assessment device with indoor positioning was practical and provided new knowledge on direct reading exposure assessment methods.CC999999/Intramural CDC HHS/United States2017-01-01T00:00:00Z26786234PMC506836

Real-time monitoring and warning system in urban rivers

Urban rivers water quality is not suitable for use. The volume of river water in the city is fast full when it rains. Both of these problems need to be monitored. The purpose of monitored to give a warning to a community around the rivers. The rivers water quality determined base on the pH sensor, and turbidity sensor detection. The river water level is determined based on the results of ultrasonic sensor readings. The reading of three sensors is sent via GSM (General Service Mobile) communication network in SMS (Short Message Service) form. The reading also sent via internet data communication network to the server and displayed on web page form. This study indicates that all three sensors are able to detect pH, turbidity, and surface level of the river. The Sensors reading delivered via the GSM communication network, it provides real-time river water information. Whereas sensor readings sent via data communication networks provide river water information that is not real-time. Thus, sensor readings of water urban rivers better delivered via GSM on SMS form than via data communication on Web page form

Une lecture probabiliste du cycle d’affaires américain

This paper explores 35 years of the American business cycle with the Hidden Markov Model (HMM) as a monitoring tool using monthly data. It exhibits ten US time series, which offer reliable information to detect recessions in real time. It also assesses the performances of different and complementary “recession models” based on Markovian processes : the “Pooled data model” and a multivariate HMM, and draws two main conclusions: simple HMM are decisive to monitor the business cycle providing that the series are proved highly reliable; models adding a multivariate dimension are useful but work marginally better than a simple summary : the inner quality of series seem to dominate their modeling. This paper introduces a new reading of the business cycle through, a favored recession model and concludes about leading and “real time detection” limitations. This paper is written in French.Business Cycle, Markov Switching, MSVAR, Real time data vintage, Coincident Indicators, Recession, NBER dating

Assessment of SARS-CoV-2 RNA shedding in semen of 36 males with symptomatic, asymptomatic, and convalescent infection during the first and second wave of COVID-19 pandemic in Italy

: The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) receptor, angiotensin-converting enzyme 2 (ACE2), has been identified in the human testis, but the risk of transmission of SARS-CoV-2 through sexual intercourse still needs to be defined. The goal of our study was to determine if SARS-CoV-2 is detectable in the semen of patients suffering or recovering from coronavirus disease-19 (COVID-19), still testing positive at nasopharyngeal swabs but showing mild or no symptoms at the time of sampling. Detection of SARS-CoV-2 RNA in semen was performed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR) and nested PCR targeting open reading frame (ORF) 1ab. Medical history of the enrolled patients was taken, including COVID-19-correlated symptoms, both at the time of diagnosis and at the time of interview. Results of real-time RT-PCR and nested PCR in semen showed no evidence of SARS-CoV-2 RNA in the 36 patients suffering or recovering from COVID-19 but still positive in a nasopharyngeal swab, from over 116 patients enrolled in the study. SARS-CoV-2 detection and persistence in semen would have an impact on both clinical practice and public health strategies, but our results would suggest that SARS-CoV-2 is not present in the semen of men recovering from COVID-19

A miniaturized silicon based device for nucleic acids electrochemical detection

In this paper we describe a novel portable system for nucleic acids electrochemical detection. The core of the system is a miniaturized silicon chip composed by planar microelectrodes. The chip is embedded on PCB board for the electrical driving and reading. The counter, reference and work microelectrodes are manufactured using the VLSI technology, the material is gold for reference and counter electrodes and platinum for working electrode. The device contains also a resistor to control and measuring the temperature for PCR thermal cycling. The reaction chamber has a total volume of 20 μL. It is made in hybrid silicon–plastic technology. Each device contains four independent electrochemical cells.Results show HBV Hepatitis-B virus detection using an unspecific DNA intercalating redox probe based on metal–organic compounds. The recognition event is sensitively detected by square wave voltammetry monitoring the redox signals of the intercalator that strongly binds to the double-stranded DNA. Two approaches were here evaluated: (a) intercalation of electrochemical unspecific probe on ds-DNA on homogeneous solution (homogeneous phase); (b) grafting of DNA probes on electrode surface (solid phase).The system and the method here reported offer better advantages in term of analytical performances compared to the standard commercial optical-based real-time PCR systems, with the additional incomes of being potentially cheaper and easier to integrate in a miniaturized device. Keywords: Electrochemical detection, Real time PCR, Unspecific DNA intercalato