scholarly journals Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests

2020 ◽  
Author(s):  
Bindu Swapna Madala ◽  
Andre L. M. Reis ◽  
Ira W. Deveson ◽  
William Rawlinson ◽  
Tim R. Mercer
Keyword(s):  
Cross Validation ◽  
Diagnostic Testing ◽  
Genetic Material ◽  
Positive Control ◽  
Negative Control ◽  
Reference Standards ◽  
Rt Pcr ◽  
Standard Design ◽  
Negative Controls

ABSTRACTDNA synthesis in vitro has enabled the rapid production of reference standards. These are used as controls, and allow measurement and improvement of the accuracy and quality of diagnostic tests. Current reference standards typically represent target genetic material, and act only as positive controls to assess test sensitivity. However, negative controls are also required to evaluate test specificity. Using a pair of chimeric A/B RNA standards, this allowed incorporation of positive and negative controls into diagnostic testing for the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The chimeric standards constituted target regions for RT-PCR primer/probe sets that are joined in tandem across two separate synthetic molecules. Accordingly, a target region that is present in standard A provides a positive control, whilst being absent in standard B, thereby providing a negative control. This design enables cross-validation of positive and negative controls between the paired standards in the same reaction, with identical conditions. This enables control and test failures to be distinguished, increasing confidence in the accuracy of results. The chimeric A/B standards were assessed using the US Centers for Disease Control real-time RT-PCR protocol, and showed results congruent with other commercial controls in detecting SARS CoV-2 in patient samples. This chimeric reference standard design approach offers extensive flexibility, allowing representation of diverse genetic features and distantly related sequences, even from different organisms.

scholarly journals Chimeric synthetic reference standards enable cross-validation of positive and negative controls in SARS-CoV-2 molecular tests

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bindu Swapna Madala ◽  
Andre L. M. Reis ◽  
Ira W. Deveson ◽  
William Rawlinson ◽  
Tim R. Mercer
Keyword(s):  
Cross Validation ◽  
Diagnostic Testing ◽  
Genetic Material ◽  
Positive Control ◽  
Negative Control ◽  
Reference Standards ◽  
Rt Pcr ◽  
Standard Design ◽  
Negative Controls

AbstractDNA synthesis in vitro has enabled the rapid production of reference standards. These are used as controls, and allow measurement and improvement of the accuracy and quality of diagnostic tests. Current reference standards typically represent target genetic material, and act only as positive controls to assess test sensitivity. However, negative controls are also required to evaluate test specificity. Using a pair of chimeric A/B RNA standards, this allowed incorporation of positive and negative controls into diagnostic testing for the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The chimeric standards constituted target regions for RT-PCR primer/probe sets that are joined in tandem across two separate synthetic molecules. Accordingly, a target region that is present in standard A provides a positive control, whilst being absent in standard B, thereby providing a negative control. This design enables cross-validation of positive and negative controls between the paired standards in the same reaction, with identical conditions. This enables control and test failures to be distinguished, increasing confidence in the accuracy of results. The chimeric A/B standards were assessed using the US Centres for Disease Control real-time RT-PCR protocol, and showed results congruent with other commercial controls in detecting SARS-CoV-2 in patient samples. This chimeric reference standard design approach offers extensive flexibility, allowing representation of diverse genetic features and distantly related sequences, even from different organisms.

scholarly journals Evaluation of ionic degradation and slot corrosion of metallic brackets by the action of different dentifrices

2013 ◽  
Vol 18 (1) ◽  
pp. 86-93
Author(s):  
Gustavo Antônio Martins Brandão ◽  
Rafael Menezes Simas ◽  
Leandro Moreira de Almeida ◽  
Juliana Melo da Silva ◽  
Marcelo de Castro Meneghim ◽  
...  
Keyword(s):  
Chemical Composition ◽  
Artificial Saliva ◽  
Positive Control ◽  
Negative Control ◽  
Sem Analysis ◽  
Wilcoxon Test ◽  
Surface Polishing ◽  
Aluminium Ion ◽  
Negative Controls

OBJECTIVE: To evaluate the in vitro ionic degradation and slot base corrosion of metallic brackets subjected to brushing with dentifrices, through analysis of chemical composition by Energy Dispersive Spectroscopy (EDS) and qualitative analysis by Scanning Electron Microscopy (SEM). METHODS: Thirty eight brackets were selected and randomly divided into four experimental groups (n = 7). Two groups (n = 5) worked as positive and negative controls. Simulated orthodontic braces were assembled using 0.019 x 0.025-in stainless steel wires and elastomeric rings. The groups were divided according to surface treatment: G1 (Máxima Proteção Anticáries®); G2 (Total 12®); G3 (Sensitive®); G4 (Branqueador®); Positive control (artificial saliva) and Negative control (no treatment). Twenty eight brushing cycles were performed and evaluations were made before (T0) and after (T1) experiment. RESULTS: The Wilcoxon test showed no difference in ionic concentrations of titanium (Ti), chromium (Cr), iron (Fe) and nickel (Ni) between groups. G2 presented significant reduction (p < 0.05) in the concentration of aluminium ion (Al). Groups G3 and G4 presented significant increase (p < 0.05) in the concentration of aluminium ion. The SEM analysis showed increased characteristics indicative of corrosion on groups G2, G3 and G4. CONCLUSION: The EDS analysis revealed that control groups and G1 did not suffer alterations on the chemical composition. G2 presented degradation in the amount of Al ion. G3 and G4 suffered increase in the concentration of Al. The immersion in artificial saliva and the dentifrice Máxima Proteção Anticáries® did not alter the surface polishing. The dentifrices Total 12®, Sensitive® and Branqueador® altered the surface polishing.

scholarly journals Indonesian Strain of Lactobacillus reuteri Probiotic Reduces the Initial Biofilm Colonization

2020 ◽  
Vol 14 (1) ◽  
pp. 544-553
Author(s):  
Armelia Sari Widyarman ◽  
Triska Ramajayanti ◽  
Citra Fragrantia Theodorea
Keyword(s):  
Streptococcus Mutans ◽  
Biofilm Formation ◽  
Lactobacillus Reuteri ◽  
Positive Control ◽  
Negative Control ◽  
Microbial Biofilms ◽  
Incubation Periods ◽  
Negative Controls ◽  
Initial Biofilm

Background: The benefits of probiotics for human health have long been proven. Probiotic Lactobacillus reuteri, can produce a beneficial broad-spectrum antibacterial compound called reuterin by metabolizing glycerol. Objective: The aim of the study was to investigate the effect of the Indonesian strain of L. reuteri LC382415 on mono- and dual-species Streptococcus mutans and Streptococcus sanguinis biofilms in vitro. Methods: Streptococcus mutans and S. sanguinis were cultured in BHI broth. Lactobacillus reuteri LC382415 was inoculated on MRS agar. The different concentrations effect of L. reuteri (1×104, 1×106, and 1×108 CFU/mL) with and without glycerol supplementation on microbial biofilms were examined using a biofilm assay after incubation for 1,3,6, and 24-h. The biofilm mass optical density was measured with a microplate spectrophotometer at 490 nm. Chlorhexidine gluconate (0.2%) was used as a positive control, and wells without treatment were used as negative controls. Results: A significant reduction in mono- and dual-species S. mutans and S. sanguinis biofilm formation was observed after treatment with all concentrations of L.reuteri and after all incubation periods (p<0.05) with or without glycerol supplementation. The concentration of 1×104 CFU/mL after 3-h incubation was the most effective in inhibiting biofilm formation, with 87.8% S. mutans, 95.9% S. sanguinis, and 80.4% dual-species biofilm reduction compared to the negative control (p<0.05). Conclusion: The Indonesian strain of L. reuteri effectively reduces mono- and dual-species S.mutans and S. sanguinis biofilms. This suggests that it may be useful in preventing biofilm formation in oral cavities. Future studies on the mechanism of action of this active component are warranted.

scholarly journals UJI EFEKTIVITAS ANTIBAKTERI EKSTRAK DAUN SIRSAK (ANNONA MURICATA LINN.) TERHADAP BAKTERI PROPIONIBACTERIUM ACNES

2019 ◽  
Vol 6 (1) ◽  
pp. 65
Author(s):  
Yurlina Zai ◽  
Agnes Yohana Kristino ◽  
Sri Lestari Ramadhani Nasution ◽  
Oliviti Natali
Keyword(s):  
Leaf Extract ◽  
Propionibacterium Acnes ◽  
Inhibition Zone ◽  
Positive Control ◽  
Negative Control ◽  
Diffusion Method ◽  
Annona Muricata ◽  
Research Model ◽  
Negative Controls

This research aims to determine the effectiveness of the antibacterial soursop leaf extract (Annona muricata L.). The method used is the agar diffusion method. The leaves were extracted by maceration method, using ethanol as a solvent. The soursop leaf extract obtained was then diluted using ethanol 96% at a concentration of 20%, 40%,60%, 80%. Positive control using clindamycin and negative controls using sterile aquadest. The research model used in this study is an experimental research model In Vitro of type. The results showed that soursop leaf extract had antibacterial effectiveness against Propionibacterium acnes with an average inhibition zone diameter of 9,7 mm; 13,7 mm; 15,7 mm; 16,3 mm; positive control (clindamysin) 21,0 mm; and negative control (aquadest) have no value tobe able to inhibit bacterial growth.

scholarly journals Ovicidal and Larvicidal Activities of Saba senegalensis (A.DC) Pichon (Apocynaceae) Extracts and Fractions on Heligmosomoides bakeri (Nematoda, Heligmosomatidae)

2019 ◽  
pp. 1-13
Author(s):  
Mohamed Bonewendé Belemlilga ◽  
Aristide Traoré ◽  
Lazare Belemnaba ◽  
Félix Bondo Kini ◽  
Sylvin Ouédraogo ◽  
...  
Keyword(s):  
Larvicidal Activity ◽  
Larval Survival ◽  
Positive Control ◽  
Negative Control ◽  
Heligmosomoides Bakeri ◽  
Saba Senegalensis ◽  
Larvicidal Activities ◽  
Negative Controls ◽  
Eggs And Larvae

Aims: To investigate ovicidal and larvicidal activities of an aqueous decoction (AD) and hydroethanolic macerate (HEM) extracts and fractions of the leaves of Saba senegalensis. Study Design: In vitro, the ovicidal and larvicidal activities of AD and HEM extracts and fractions of the leaves of Saba senegalensis on the eggs and larvae (L1) of Heligmosomoides bakeri. Place and Duration of Study: The experiment was conducted at the department of Medicine and Traditional Pharmacopeia-Pharmacy (MEPHATRA-PH) of Institute of Research in Health Sciences (IRSS) between June 2015 and December 2016. Methodology: The phytochemical groups of the extract and fractions of Saba senegalensis were determined by a colorimetric and Thin Layer Chromatography methods. The eggs were obtained from feces of mice deliberately infected and the larvae from the eggs were incubated at 25 ±2℃ for 72 hours. Eggs and larvae were exposed to increasing concentrations (100; 625; 1250; 2500; 3750 µg/mL) of the different extracts, 48 hours and 24 hours for the eggs and larvae respectively. Distilled water and DMSO 0.1% were used as negative controls while albendazole and levamisole were used as positive controls. Results: The phytochemical groups of interest are the tannins, saponins, flavonoids and triterpenes. The negative control had given 2.16% of egg hatch inhibition and 0% of larvae mortality mean while the positive control had given 100% in both cases. The extracts inhibited eggs hatching and affected larval survival. Pharmacological effects were concentration-dependent. The ovicidal and larvicidal activity of HEM is more interesting than that of AD with an Emax = 95.60% and an IC50 = 390 µg/mL. It is the same for the larvicidal activity with Emax = 100% and an LC50 = 900 µg/mL.  However, the differences were not statistically significant. Conclusion: These results show the ovicidal and larvicidal properties of the S. senegalensis leaves.

scholarly journals EFFECT OF CURCUMA XANTHORRHIZA ROXB. ETHANOL EXTRACT ON THE VIABILITY OF STREPTOCOCCUS MUTANS AND STREPTOCOCCUS SANGUINIS DUAL-SPECIES BIOFILMS

2019 ◽  
pp. 75-78
Author(s):  
FARIDA ERVINTARI ◽  
RIA PUSPITAWATI ◽  
SRI UTAMI
Keyword(s):  
Streptococcus Mutans ◽  
Bacterial Culture ◽  
Ethanol Extract ◽  
Positive Control ◽  
Negative Control ◽  
Streptococcus Sanguinis ◽  
Curcuma Xanthorrhiza ◽  
Ethanol Extracts ◽  
Negative Controls

Objective: This study aimed to determine the effect of ethanol Curcuma extract on the viability of S. mutans and Streptococcus sanguinis in a dualspeciesin vitro biofilm model.Methods: Dual-species biofilms of S. mutans and S. sanguinis were exposed to ethanol Curcuma extract at various concentrations. The sample ofsaliva was gathered from healthy volunteers. Chlorhexidine 0.2% was used as a positive control, and bacterial culture without intervention servedas a negative control. The total suspensions of 10−as were prepared for S. mutans and S. sanguinis cells. The bacteria were incubated for 20 h (activematuration phase) and 24 h (maturation phase).Results: The result showed decreased S. mutans and S. sanguinis viability after exposure to 0.2%–25% Curcuma ethanol extracts during the activeaccumulation and maturation phases. The decrease in bacterial viability was significantly different in all concentrations of Curcuma ethanol extractscompared with negative controls (p<0.05) in the active accumulation and maturation phases.Conclusion: Temulawak ethanol extract (starting at 0.2%) can decrease the viability of S. mutans and S. sanguinis in a dual species in vitro biofilmmodel during the accumulation and maturation phases.

scholarly journals Effectiveness of Casein Phosphopeptide-Amorphous Calcium Phosphate (CPP-ACP) Compared to Fluoride Products in an In-Vitro Demineralization Model

Materials ◽  
2021 ◽  
Vol 14 (20) ◽  
pp. 5974
Author(s):  
Markus Reise ◽  
Stefan Kranz ◽  
Markus Heyder ◽  
Klaus D. Jandt ◽  
Bernd W. Sigusch
Keyword(s):  
Calcium Phosphate ◽  
Amorphous Calcium Phosphate ◽  
Polarized Light ◽  
Positive Control ◽  
Negative Control ◽  
Control Groups ◽  
Casein Phosphopeptide ◽  
Tooth Mousse ◽  
Negative Controls

The goal of this study was to evaluate the effectiveness of the toothpaste Tooth Mousse compared to conventional fluoride-based versions in the prevention of enamel and dentin demineralization. Human enamel and dentin samples (n = 120 each) were exposed to artificial demineralization at pH 4.92. During the demineralization process, the samples in the test groups were periodically treated with Tooth Mousse (TM) containing casein-phosphopeptide -amorphous-calcium-phosphate (CPP-ACP) and Tooth Mousse Plus (TMP) containing amorphous-calcium-fluoride-phosphate (CPP-ACPF) to evaluate their protective properties. Fluoride toothpastes containing 1400 ppm amine fluoride (AmF) and 1450 ppm sodium fluoride (NaF) were applied in the positive control groups. Treatment with distilled water (group C-W) or demineralization without treatment (group C-D) served as negative controls. After the demineralization and treatment process, all samples were cut longitudinally and lesion depths were determined at six locations using polarized light microscopy. In TM/TMP groups (enamel: 80/86 µm, dentin: 153/156 µm) lesion depths were significantly smaller compared to the negative control groups C-W/C-D (enamel: 99/111 µm, dentin: 163/166 µm). However, TM and TMP compared to the positive controls AmF/NaF (enamel: 58/63 µm, dentin: 87/109 µm) showed higher lesion depths. The application of TM/TMP (89%/78%) during demineralization led to a reduced number of severe lesions compared to the negative controls C-W/C-D (100%/95%). In this study we demonstrate that Tooth Mousse is less effective regarding prevention of enamel and dentin demineralization compared to fluoride containing toothpastes.

Aktivitas Antifungi Air Perasan Bawang Merah (Allium ascalonicum L.) Terhadap Candida albicans Secara In Vitro

2017 ◽  
Vol 9 (2) ◽  
pp. 71
Author(s):  
Nurhasanah Nurhasanah ◽  
Fauzia Andrini ◽  
Yulis Hamidy
Keyword(s):  
Candida Albicans ◽  
Antifungal Activity ◽  
Allium Sativum ◽  
Fungicidal Activity ◽  
Positive Control ◽  
Negative Control ◽  
Randomized Design ◽  
Significant Difference ◽  
Completely Randomized Design

Shallot (Allium ascalonicum L.) has been known as traditional medicine. Shallot which has same genus with garlic(Allium sativum L.) contains allicin that is also found in garlic and has been suspected has fungicidal activity toCandida albicans. It is supported by several researches. Therefore, shallot is suspected has antifungal activity too.The aim of this research was to know antifungal activity of shallot’s water extortion againsts Candida albicans invitro. This was a laboratory experimental research which used completely randomized design, with diffusion method.Shallot’s water extortion was devided into three concentrations, there were 50%, 100% and 200%. Ketoconazole 2%was positive control and aquadest was negative control. The result of this research based on analysis of varians(Anova), there was significant difference between several treatments and was confirmed with Duncan New MultipleRange Test (DNMRT) p<0,05, there was significant difference between 100% shallot’s water extortion with othertreatments, but there was no significant difference between 50% shallot’s water extortion with 200% shallot’s. Theconclusion was shallot’s water extortion had antifungal activity againsts Candida albicans with the best concentration100%, but it was lower than ketoconazole 2%.

scholarly journals Investigation of potential anti-urolithiatic activity from different types of Musa pseudo-stem extracts in inhibition of calcium oxalate crystallization

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Mazni Abu Zarin ◽  
Joo Shun Tan ◽  
Paramasivam Murugan ◽  
Rosma Ahmad
Keyword(s):  
Calcium Oxalate ◽  
Incubation Time ◽  
Positive Control ◽  
Negative Control ◽  
Aggregation Assay ◽  
Banana Tree ◽  
Methanolic Extracts ◽  
Different Types ◽  
Aggregation Activity

Abstract Background The banana or scientifically referred to as Musa sp., is one of the most popular fruits all over the world. Almost all parts of a banana tree, including the fruits, stem juice, and flowers are commonly used as traditional medicine for treating diarrhoea (unripe), menorrhagia, diabetes, dysentery, and antiulcerogenic, hypoglycemic, antilithic, hypolipidemic conditions, plus antioxidant actions, inflammation, pains and even snakebites. The study carried out was to evaluate in vitro anti-urolithiatic activity from different types of Musa pseudo-stems. Methods Observing anti-urolithiathic activity via in vitro nucleation and aggregation assay using a spectrophotometer followed by microscopic observation. A total of 12 methanolic extracts were tested to determine the potential extracts in anti-urolithiasis activities. Cystone was used as a positive control. Results The results manifested an inhibition of nucleation activity (0.11 ± 2.32% to 55.39 ± 1.01%) and an aggregation activity (4.34 ± 0.68% to 58.78 ± 1.81%) at 360 min of incubation time. The highest inhibition percentage in nucleation assay was obtained by the Musa acuminate x balbiciana Colla cv “Awak Legor” methanolic pseudo-stem extract (2D) which was 55.39 ± 1.01%at 60 min of incubation time compared to the cystone at 30.87 ± 0.74%. On the other hand,the Musa acuminate x balbiciana Colla cv “Awak Legor” methanolic bagasse extract (3D) had the highest inhibition percentage in the aggregation assay incubated at 360 min which was obtained at 58.78 ± 1.8%; 5.53% higher than the cystone (53.25%).The microscopic image showed a great reduction in the calcium oxalate (CaOx) crystals formation and the size of crystals in 2D and 3D extracts, respectively, as compared to negative control. Conclusions The results obtained from this study suggest that the extracts are potential sources of alternative medicine for kidney stones disease.

In vitro insecticidal effect of commercial fatty acids, ß-sitosterol and rutin against the sugarcane aphid, Melanaphis sacchari Zehntner (Hemiptera: Aphididae)

2022 ◽  
Author(s):  
Liliana Aguilar Marcelino ◽  
Jesús Antonio Pineda Alegría ◽  
David Osvaldo Salinas-Sánchez ◽  
Víctor Manuel Hernández Velázquez ◽  
Gonzalo Iván Silva Aguayo ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Positive Control ◽  
Negative Control ◽  
Tween 20 ◽  
Agricultural Pests ◽  
Melanaphis Sacchari ◽  
Insecticidal Effect ◽  
Sugarcane Aphid ◽  
Alternative Means

The sugarcane aphid, Melanaphis sacchari Zehntner (Hemiptera: Aphididae), is the main pest of sorghum, Sorghum bicolor L. Moench (Poaceae), in Mexico. To control this insect, farmers currently use synthetic chemical insecticides, which are toxic to humans and biodiversity. However, natural products are a promising potential source of safer alternative means to control different agricultural pests. The main objective of this study was to evaluate the insecticidal effect of contact by fumigation of pure molecules of four commercial fatty acids (palmitic, stearic, pentadecanoic and linoleic acids), the phytosterol ß -sitosterol, and the flavonoid rutin. The results showed that fatty acids were the most effective against M. sacchari ; the highest mortality rate (85%) was produced by linoleic acid and the LC 50 was 1,181 ppm, followed by stearic and palmitic acids with mortality percentages of 74 and 63%, respectively, at a concentration of 2,500 ppm at 72 h. The positive control, imidacloprid, had 100% mortality in 24 h and the tween 20 negative control exhibited 4% mortality in 72 h. Our results show that commercial fatty acids are effective against adults of M. sacchari , and can be considered an environmentally friendly alternative to the frequent use of synthetic chemical insecticides.

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