scholarly journals Wide Application of Minimally Processed Saliva on Multiple RT-qPCR Kits for SARS-CoV-2 Detection in Indonesia

Author(s):  
Caroline Mahendra ◽  
Maria Mardalena Martini Kaisar ◽  
Suraj Rajan Vasandani ◽  
Sem Samuel Surja ◽  
Enty Tjoa ◽  
...  

Saliva as a sample matrix has been an attractive alternative for the detection of SARS-CoV-2. However, due to potential variability in collection and processing steps, evaluating a proposed workflow amongst the local population is recommended. Here, we aim to validate the collection and treatment of human saliva as a direct specimen for RT-qPCR-based detection of SARS-CoV-2 in Indonesia. We demonstrated that SARS-CoV-2 target genes were detected in saliva specimens and remained stable for five days either refrigerated or stored at room temperature. The method of processing saliva specimens described in this report bypasses the need for an RNA-extraction process, thereby reducing the cost, time, and manpower required for processing samples. The developed method was tested across nine commercial kits, including the benchmark, to demonstrate its wide applicability on multiple existing workflows. Our developed method achieved an 86% overall agreement rate compared to paired nasopharyngeal and oropharyngeal swab specimens (NPOP). With the assistance of a saliva sampling device, the collection was found to be more convenient for individuals and improved the overall agreement rate to 97%.

2021 ◽  
Author(s):  
Caroline Mahendra ◽  
Maria M. M. Kaisar ◽  
Suraj R. Vasandani ◽  
Sem Samuel Surja ◽  
Enty Tjoa ◽  
...  

Saliva as a sample matrix has been an attractive alternative for the detection of SARS-CoV-2. However, due to potential variability in collection and processing steps, it is recommended to evaluate a proposed workflow amongst the local population. Here, we aim to validate collection and treatment of human saliva as a direct specimen for RT-qPCR based detection of SARS-CoV-2 in Indonesia. We demonstrated that SARS-CoV-2 target genes were detected in saliva specimen and remained stable for five days refrigerated or room temperature storage. The method of processing saliva specimen described in this report is free from RNA-extraction step, thereby reduces cost, time, and manpower required for processing samples. The developed method was validated for use on three COVID-19 RT-PCR kits commercially available. Our developed method achieved 85% agreement rate when compared to paired nasopharyngeal and oropharyngeal swab specimens (NPOP). With the assistance of a specimen sampling device, QuickSpit(TM), collection was found to be more convenient for individuals and improved agreement rate to 90%.


Author(s):  
Lifeng Zhou ◽  
Arun Richard Chandrasekaran ◽  
Jibin Abraham Punnoose ◽  
Gaston Bonenfant ◽  
Stephon Charles ◽  
...  

AbstractViral detection is critical for controlling disease spread and progression. Recent emerging viral threats including Zika, Ebola, and the current COVID-19 outbreak highlight the cost and difficulty in responding rapidly. To address these challenges, we develop a platform for low-cost and rapid detection of viral RNA with DNA nanoswitches designed to mechanically reconfigure in response to specific viruses. Using Zika virus as a model system, we show non-enzymatic detection of viral RNA to the attomole level, with selective and multiplexed detection between related viruses and viral strains. For clinical-level sensitivity in biological fluids, we paired the assay with a sample preparation step using either RNA extraction or isothermal pre-amplification. Our assay can be performed with minimal or no lab infrastructure, and is readily adaptable to detect other viruses. We demonstrate the adaptability of our method by quickly developing and testing DNA nanoswitches for detecting a fragment of SARS-CoV-2 RNA in human saliva. Given this versatility, we expect that further development and field implementation will improve our ability to detect emergent viral threats and ultimately limit their impact.


2021 ◽  
Vol 2 (2) ◽  
pp. 325-334
Author(s):  
Neda Javadi ◽  
Hamed Khodadadi Tirkolaei ◽  
Nasser Hamdan ◽  
Edward Kavazanjian

The stability (longevity of activity) of three crude urease extracts was evaluated in a laboratory study as part of an effort to reduce the cost of urease for applications that do not require high purity enzyme. A low-cost, stable source of urease will greatly facilitate engineering applications of urease such as biocementation of soil. Inexpensive crude extracts of urease have been shown to be effective at hydrolyzing urea for carbonate precipitation. However, some studies have suggested that the activity of a crude extract may decrease with time, limiting the potential for its mass production for commercial applications. The stability of crude urease extracts shown to be effective for biocementation was studied. The crude extracts were obtained from jack beans via a simple extraction process, stored at room temperature and at 4 ℃, and periodically tested to evaluate their stability. To facilitate storage and transportation of the extracted enzyme, the longevity of the enzyme following freeze drying (lyophilization) to reduce the crude extract to a powder and subsequent re-hydration into an aqueous solution was evaluated. In an attempt to improve the shelf life of the lyophilized extract, dextran and sucrose were added during lyophilization. The stability of purified commercial urease following rehydration was also investigated. Results of the laboratory tests showed that the lyophilized crude extract maintained its activity during storage more effectively than either the crude extract solution or the rehydrated commercial urease. While incorporating 2% dextran (w/v) prior to lyophilization of the crude extract increased the overall enzymatic activity, it did not enhance the stability of the urease during storage.


Metabolites ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 240
Author(s):  
Alison Woodward ◽  
Alina Pandele ◽  
Salah Abdelrazig ◽  
Catherine A. Ortori ◽  
Iqbal Khan ◽  
...  

The integration of untargeted metabolomics and transcriptomics from the same population of cells or tissue enhances the confidence in the identified metabolic pathways and understanding of the enzyme–metabolite relationship. Here, we optimised a simultaneous extraction method of metabolites/lipids and RNA from ependymoma cells (BXD-1425). Relative to established RNA (mirVana kit) or metabolite (sequential solvent addition and shaking) single extraction methods, four dual-extraction techniques were evaluated and compared (methanol:water:chloroform ratios): cryomill/mirVana (1:1:2); cryomill-wash/Econospin (5:1:2); rotation/phenol-chloroform (9:10:1); Sequential/mirVana (1:1:3). All methods extracted the same metabolites, yet rotation/phenol-chloroform did not extract lipids. Cryomill/mirVana and sequential/mirVana recovered the highest amounts of RNA, at 70 and 68% of that recovered with mirVana kit alone. sequential/mirVana, involving RNA extraction from the interphase of our established sequential solvent addition and shaking metabolomics-lipidomics extraction method, was the most efficient approach overall. Sequential/mirVana was applied to study a) the biological effect caused by acute serum starvation in BXD-1425 cells and b) primary ependymoma tumour tissue. We found (a) 64 differentially abundant metabolites and 28 differentially expressed metabolic genes, discovering four gene-metabolite interactions, and (b) all metabolites and 62% lipids were above the limit of detection, and RNA yield was sufficient for transcriptomics, in just 10 mg of tissue.


Author(s):  
Susan Elizabeth Hough ◽  
Roger G. Bilham

The reduction of an entire city to a pile of rubble poses a special problem for the survivors. Roads are blocked, underground pipes are broken, and disease accompanies the decay of incompletely buried bodies. Fresh water and sewage no longer flow, food becomes scarce, and the absence of shelter from extremes of temperature can make life miserable. In the cities of the ancient world a very real practical problem followed in the months and years after the destruction of a city—a cleanup operation beyond the wildest dreams of the survivors. Although steam shovels had been used for moving heavy materials in building the Suez and Panama canals in 1869 and 1910, respectively, it was not until 1923 that the bulldozer was invented. The even more useful backhoe followed 25 years later. Thus, clearing debris was a daunting task as recently as the 1906 San Francisco earthquake. In his book The City That Is: The Story of the Rebuilding of San Francisco in Three Years, Rufus Steele wrote of the rebuilding effort: . . . First the ground had to be cleared. The task would have baffled Hercules— cleaning out the Augean stables was the trick of a child compared to clearing for the new city. This is a step in the rebuilding which fails entirely to impress the visitor of today. He can form no conception of the waste which had to be reduced to bits and then lifted and carted away to the dumping grounds. The cost of removing it was more than twenty million dollars. . . . Lacking what we would now consider modern machinery to move large volumes of debris, the rebuilders of San Francisco extended railway lines across town, brought in steam and electric cranes, and relied heavily on teams of horses that suddenly found themselves in enormous demand. According to Steele, “Huge mechanical devices for shoveling and loading were invented and set to work.” Formidable as the task may have been, San Francisco tapped into several critical resources in its Herculean efforts: trains, cranes, and, perhaps most important, large numbers of survivors following an earthquake that killed a very small fraction of the local population.


2019 ◽  
Vol 43 ◽  
Author(s):  
Rafael Novais de Miranda ◽  
Caroline Marcela da Silva ◽  
Antonio Carlos da Mota Porto ◽  
Welison Andrade Pereira

ABSTRACT The Straw Test is an assay developed to evaluate the resistance of common bean to white mold, in which the plant stems are inoculated and the symptoms of the disease are monitored. It is plausible to admit that investigating gene expression in pathogen-infected tissues may be strategically interesting. However, obtaining a quality RNA is a basic requirement for this purpose. Therefore, the objective of this study was to evaluate adjustments in protocols of commercial kits in the expectation of improving the quality of RNA obtained from bean stems. For this, plants of two lines were inoculated and the stems pathogen-infected were collected 72 hours after. For RNA extraction, two commercial reagents were used following the manufacturer’s recommendations and then following adaptations in these protocols. In particular, the proposed modifications relate to volumes of supernatant recovered in purification steps, additional step of chloroform purification and extended time for nucleic acids precipitation. The obtained RNA was analyzed by spectrophotometer, electrophoresis and bioanalyzer, then converted into cDNA and subsequently submitted to PCR. From the obtained data, it was observed that the adaptations made in the protocols contributed to better results and that, when the indicative values of RNA quality are guaranteed, the subsequent reactions are more pure, precise and representative.


Energies ◽  
2019 ◽  
Vol 12 (15) ◽  
pp. 2866
Author(s):  
Andong Yin ◽  
Shenchun Wu ◽  
Weihan Li ◽  
Jinfang Hu

As an attractive alternative to the traditional plug-in charged electric vehicles (EVs), wireless-charged EVs have recently been in the spotlight. Opportunistically charged utilizing the wireless-charging infrastructure installed under the road at bus stops, an electric bus can have a smaller and lighter battery pack. In this paper, an improved opportunistic wireless-charging system (OWCS) for electric bus is introduced, which includes the opportunistic stationary wireless-charging system (OSWCS) and opportunistic hybrid wireless-charging system (OHWCS) consisting of stationary wireless-charging and dynamic wireless-charging. A general battery reduction model is established for the opportunistic wireless-charged electric bus (OWCEB). Two different battery-reduction models are built separately for OWCEB on account of the characteristics of OSWCS and OHWCS. Additionally, the cost saving models including the production cost saving, the operation cost saving and total cost saving are established. Then, the mathematical models are demonstrated with a numerical example intuitively. Furthermore, we analyze several parameters that influence the effectiveness of battery reduction due to the application of an opportunistic wireless-charging system on an electric bus. Finally, some points worth discussing in this work are performed.


2013 ◽  
Vol 25 (1) ◽  
pp. 248
Author(s):  
A. A. P. Derussi ◽  
A. C. S. Castilho ◽  
R. W. A. Souza ◽  
R. Volpato ◽  
C. R. F. Guaitolini ◽  
...  

The aim of this study was to compare the mRNA levels of hormone receptor for progesterone (PR), oestrogen α (ER-α), oestrogen β (ER-β), and oxytocin (OTR) in canine morulae and blastocysts. Ten healthy mature bitches were inseminated based on monitoring vaginal cytology and progesterone concentration. The first insemination was performed on Day 2 after the preovulatory LH surge (progesterone 4 ng mL–1), and the second was performed 48 h later. All females were submitted to ovariohysterectomy (OVH), and the oviduct as well the uterurs were flushed with PBS solution to obtain the embryos. The females were divided into two groups: Group A (n = 5), morulae were collected 8 days after the LH surge and Group B (n = 5), blastocysts were collected 12 days after the LH surge. The pools (n = 10) of embryos (5 embryos/pool) were stored in RNAlater® (Ambion, Life Technologies, USA) at –80°C. The samples were analysed together. The RNA later was removed used PBS calcium free and the total RNA extraction was performed using the Qiagen RNeasy micro-kit (Hildesheim, Germany). Before reverse-transcription (RT) reaction, the total RNA was treated with DNase I Amplification Grade (Invitrogen Life Technologies, Carlsbad, CA, USA). The gene expression of target genes was assessed by real-time RT-qPCR, using SuperScript III for RT and power SYBR Green PCR Master Mix (Applied Biosystems, USA) for cDNA for PCR. The primers for target genes were designed using the software Primer Express® (Applied Biosystems, USA). The gene expression of target genes was normalized by HPRT gene and the relative abundance of mRNA was determined by the ΔΔct method corrected by amplification efficiency using Pffafl’s equation. The means of mRNA relative abundance were compared by t-test. The PR mRNA expression only in blastocysts is similar to the results obtained by Hou et al. (1997) in rat embryos. It is believed that the absence of PR in the early stages of cleavage is due to the indirect action of progesterone by growth factors produced by the maternal reproductive tract (2). Apparently, ER-β action does not occur in the embryo canine phases analysed; however, the action of ER-α seems related to the deployment signal as seen by Hou et al. (1996) in rats. Similarly to findings in the literature, OTR expression decreased in canine embryonic development. This receptor was produced by blastocysts while present in the uterus, which may represent an incidental mechanism to the embryo control of endometrial receptivity, such as also to prevent the development of endometrial luteolytic mechanism. The variation in hormone receptors gene expression in canine embryos can be influencing the transition from morula to blastocyst. In addition, a hormonal influence on these structures can occur in different ways.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Aniela Wozniak ◽  
Ariel Cerda ◽  
Catalina Ibarra-Henríquez ◽  
Valentina Sebastian ◽  
Grace Armijo ◽  
...  

Abstract The technique RT-qPCR for viral RNA detection is the current worldwide strategy used for early detection of the novel coronavirus SARS-CoV-2. RNA extraction is a key pre-analytical step in RT-qPCR, often achieved using commercial kits. However, the magnitude of the COVID-19 pandemic is causing disruptions to the global supply chains used by many diagnostic laboratories to procure the commercial kits required for RNA extraction. Shortage in these essential reagents is even more acute in developing countries with no means to produce kits locally. We sought to find an alternative procedure to replace commercial kits using common reagents found in molecular biology laboratories. Here we report a method for RNA extraction that takes about 40 min to complete ten samples, and is not more laborious than current commercial RNA extraction kits. We demonstrate that this method can be used to process nasopharyngeal swab samples and yields RT-qPCR results comparable to those obtained with commercial kits. Most importantly, this procedure can be easily implemented in any molecular diagnostic laboratory. Frequent testing is crucial for individual patient management as well as for public health decision making in this pandemic. Implementation of this method could maintain crucial testing going despite commercial kit shortages.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4727-4727
Author(s):  
Claudia Tregnago ◽  
Sanja Aveic ◽  
Elena Manara ◽  
Martina Pigazzi ◽  
Giuseppe Basso

Abstract Abstract 4727 Introduction. Transcription factors has been widely confirmed to play a central role in acute leukemia, and among them the cyclic-adenosine monophosphate response element-binding protein (CREB) was identified to be involved in triggering acute myeloid leukemia. CREB protein overexpression has been found in the bone marrow of most pediatric patients with acute leukemia, and it has been shown to induce myeloid leukemia progression in vitro and in vivo by driving the upregulation of a series of target genes. CREB is evolutionarily conserved from invertebrates to human, and although the main focus of zebrafish research has traditionally been developmental biology, this model is currently used for cancer research. In fact, tumors induced in ZF have similar morphology and activated signaling pathways of human cancers. Aim. We aimed to develop a ZF harboring CREB overexpression in myeloid precursors, and by monitoring the induced myeloid malignancy, we will characterize CREB signaling and its involvement in the myeloid transformation process. Results. Using a Multisite Gateway System we constructed a vector containing human-CREB gene fused to EGFP, driven by an early myeloid promoter, zPu.1, to induce CREB overexpression specifically in the myeloid lineage of ZF. We injected the EGFP-CREB plasmid into one-cell stage zebrafish embryos, and monitored its expression during early development. Results showed that CREB was expressed in ZF zones typical of myelopoiesis, such as in the intermediate cell mass and anterior lateral mesoderm migrating through the yolk from 12 to 48 hours post-fertilization (hpf), and few cells circulating throughout the embryo from 24 hpf. CREB transcriptional activity on cAMP response elements (CREs) was measured and confirmed by luciferase assay. The co-localization of EGFP-CREB with the CRE-mCherry reporter was seen by fluorescence microscopy analysis. To test CREB target gene expression, embryos injected with CREB or Empty vector were subjected to RNA extraction and RQ-PCR. CREB over-expression was documented (up to 103 fold), and c-myb, stat3, rb, runx1, cyclins A, B, D1 and E2 were found upregulate at 24 and 48 hpf. By RNA whole mount in situ hybridization, we revealed pu.1, mpo, gata1 and fli.1 increased signals, suggesting a general disruption of the main hematopoietic factors. Ten CREB-injected zebrafish have been grown to adulthood and all of them displayed an abnormal/sick phenotype with abdominal enlargement and swelling from 10 to 12 months. Histochemical H&E staining performed on paraffin sections revealed an abdominal tumor and metastatic infiltration in kidney, skin, gills, muscles, adipose tissue. PAS staining identified the myeloid character of the tumor mass and kidney marrow. Wright-Giemsa and ANAE staining showed the predominance of clonal monocytes on appositions of tumor mass and kidney marrow of sick ZF. Tumor mass cell sorting displayed a clonal feature of the tumor with an enrichment of the myeloid-monocitic compartment. RNA extraction from the mass shows CREB overexpression as well as its target genes (c-myb, runx1, cyclin A1, cyclin B1, cyclin B2, cyclin E1), confirming CREB involvement in this tumor formation. Conclusion. We demonstrated that CREB overexpression recapitulates myeloproliferative disorder in ZF, supporting the ZF as a suitable model for studying CREB-induced leukemia. The discovery through which targets CREB would preferentially mediate the myeloid transformation will help to unravel leukemogenesis. ZF model might be useful to test CREB directed drugs. Disclosures: No relevant conflicts of interest to declare.


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